I've noticed a lot of comments get hidden, including mine sometimes. What is the rationale for hiding them? I couldn't find the answer.
If you haven't already, you might want to check out this article on the comment privilege: https://english.stackexchange.com/help/privileges/comment -- mainly the thing to remember is that comments are transient and are really just a feedback tool to the author: clarification requests or suggestions. Once a request or suggestion is resolved, the comment trail is no longer needed, and might get cleaned up the next time the post gets reviewed.
According to this answer on Meta Stack Exchange, comments with no upvotes are hidden when the comment thread gets long. "Long" depends on the site. I don't know what "long" is set to for EL&U but possibly we could find out.
At the very beginning, when it was just Stack Overflow, there were no comments. Then, when comments were added, they were all hidden by default. Finally (but still a really long time ago), the system changed again so that the top 5 comments would be shown, for reasons explained in this blog post by "former" co-founder Jeff Atwood:
There was a grander plan with comment voting, and that plan was to promote some of the best voted comments to the question page. The default sort order is votes, descending, then date; we pick the top 5. Why did we do this?
There are often important clarifications and addendums left as comments that substantially improve the original post. It seemed a shame that these sort of comments were all locked behind the “expand comments” button, and every reader had to click on that link (or know they should click on it) to get the benefit of those comments. Information was being lost!
While I don’t want the site to devolve into a one-liner contest, some of the comments are quite witty and still on-topic. Our fellow Stack Overflow users who manage to “edutain” us deserve to have those comments seen and appreciated by a wider audience.
In an answer, Jeff elaborates that the reason for only 5 to be shown is so you "never have to read more than a page (in this case, a page is 5 comments)".
The number shown by default is still 5 on the main site, unless there are (I think) 30 or more answers posted, in which case 0-score comments are also hidden. On Meta, comments start to be hidden after 15. We have what is now the "default" hiding behavior, but sites are indeed free to change these numbers (and some have, such as The Workplace).