Actually, those books can still be read if you want to. But there are good reasons why they aren't in the canon, which I will elaborate on.
First I would like to define that "canon" means "rule". It is the standard by which we judge what is true. Any other revelation or writing is to be measured against the canon.
The books that made it into the canon were those which were known to be from early church leaders in the apostalic era.
The Shepherd of Hermas was known to have not been written until long after the apostles were gone. It was considered beneficial to read; but could never be considered canon because of it's late date.
Some like the Epistle of Barnabas were not believed to have been written by an apostalic source. It is probably not the Barnabas referenced in Acts, but was written by another Barnabas after the time of the apostles.
In the same way; writings of early church fathers like Clement were considered useful to read but could not be put on par with original apostalic writings as the rule by which other teachings and revelation are measured.
That is why you sometimes find writings like Clement or Hermas in some codex Bibles - It has always been common practice throughout church history for some bibles to include noncanonical books that were considered useful or edifying to read. Often they were put at the back of the codex. They were not intended to be considered on par with canonical scripture.
There was probably never a specific epistle to the Laodiceans in the first place. If you read Colossians 4:16 you can see that Paul is telling Colossae to send a copy of this letter to Laodicea, and in turn says a letter will be sent to Colossea from Laodicea. This very well could be referring to another of Paul's letters that had been passed to Laodicea from another church with the intention that they would copy it and forward it to Colossae. This was no doubt a common thing in the early church, where letters and gospels were copied and passed between church communities. Colossians in particular is a letter very focused on outlining overall doctrine that would be most important for all churches to have; as opposed to some other letters which were more pastoral (focused on bringing specific correction to specific issues within a church). This is also why it is speculated that perhaps the letter the Laodiceans had in their possession was the letter to the Ephesians, because that is also another overarching doctrinal letter that was likely meant to be passed between churches from the moment Paul wrote it.
Katzpur makes reference to a second epistle of Jude and other letters to the Ephesians; but I am not sure where he's getting that from. I've not yet come across anything that would suggest such things existed. I'd like if he could explain where he got that idea from.
The third letter to the Corinthians never had any widespread or early witness in Christian tradition or writings. We only have 4th century beliefs in the Syrian church that it was authentic, but they abandoned this belief not long after that based on their interaction with other regional churches (this is an example of the kind of decentralized self correction that probably took place in other instances). It was never included in the Syriac translation of the Bible before that either. You could still read it today if you want to, but I see no reason to believe it was authentic. It probably doesn't contain anything that would contradict the truth of the new testament anyway.
The Wisdom of Solomon would be considered the old testament, so it doesn't have much bearing on a discussion about the formation of the new testament canon. Roman catholic and orthodox churches today consider it useful to be read and even secondary canon, but do not put it on the same level as canonical scripture for the purpose of determining doctrine and truth.
Slight differences in early canon lists exist - but that is understandable given the decentralized way in which the scripture was copied and transferred. Authentic writings were recognized as such in the community they were received in, and then copied and passed on, but not all communities received all the writings at the same time. They would verify with other churches which writings were authentic, which is why many of the canon lists we have are in response to false writings being created long after the time of the apostles.
Ultimately, and more importantly, the same books in our new testament are accounted for and represented in these lists and recognized as scripture.
It actually gives us quite a lot of confidence in the texts; because within the early lists, compilations, and writings of the early fathers we don't see any outright heretical books like the gnostic gospels and other obvious forgeries.
Only one list makes reference to the Apocaylpse of Peter, and in that very list it says it is disputed as canonical because many don't allow it to be read in church.
However, nothing in the Apocalypse of Peter is going to change the way we view the Gospel, Jesus, or other truths in the new testament. It's not a gnostic or heretical work. So whether or not you want to believe it's canonical wouldn't really change much about the truth of the new testament. I think there's some useful things in there, but I also find other aspects of it questionable.
Revelation is well attested to have been received universally and accepted as canon by the early church and early fathers. It's objections came much later and were limited.
Jude is well referenced in the 2nd century by early church fathers and canon lists.
2 John has significant 2nd century reference as well.
Hebrews was well accepted, but in some areas it was much later disputed only because they weren't sure who wrote it. However, most in the early church said Paul had written it. We also have a 2nd century collection of Paul's letters which contains Hebrews in it.
It makes sense as why he would not state himself as the author when you realize in the book of Acts that the Jews in Jerusalem started a riot intending to kill Paul.
If Paul were to write an overall statement of faith and defense of the Gospel aimed at the community in Jerusalem; then it would make perfect sense why he would omit a greeting in order to not have the personal controversy surrounding him prevent the Jews from listening to the content contained within the letter. Paul was without a doubt one of the most, if not most, qualified person in the early church to write a document like this - not just because of his apostalic calling and high level of revelation through his relationship with the Holy Spirit, but also because he combined that with an incredible grasp of the Hebrew scriptures and Jewish law.
James and 2 Peter have allusions in the early church father's writings, but along with 3 John there is no direct reference to them in canon lists until the 3rd century. However, later writings give us a clear picture that they were widely accepted and used in the churches.
There are only a handful of new testament books that were disputed in certain areas at certain times, and of those the weakest evidence would be for only 2 Peter, 3 John, and James.
I do believe they are canonical, being an accurate witness to us of divine truth. However, even if one wanted to believe they aren't, we can still rest assured in the fact that all of the essential truth contained in the new testament does not rest on these books as their sole witness. They add depth and understanding to the truth of the new testament, but we can find the same essential truths contained in the rest of the new testament scripture.
The fact that we have the four gospels, acts, and most of Pauls writings indisputably attested to across all regions from the earliest recorded times is more than enough to firmly establish everything we believe is true. That is not to say we have any reasonable basis for questioning the canonicity of the books that don't have universal early attestation across all regions, but simply to say that we have so much universally attested to from the earliest writings that it is more than enough to establish all the fundamental truths of the Christian faith beyond doubt.
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