Did someone (a mod, I guess?) delete one of my comments for no apparent reason?
Yes, but no. The comment was deleted by a moderator, but not for no apparent reason. It was flagged and there was no good reason to keep it. Your other comment was also flagged, but this was declined as it contains a suggestion to improve the post.
As Jan pointed out, comments are not meant for eternity. (I'm personally not a huge fan of comments.) It is a routine task for us to clean them out, regularly and including our own. Usually when we have a look at a post, we read through the comments and clear whatever is distracting from the answer/ question. Most of the times these are old posts; I try to not clear any comments within the first day. Sometimes this also means merging two comments, adding a title to a link, etc. We are basically doing, what you are doing when flagging comments, only that our flag is binding from the start.
Keeping questions and answers focused is one reason why I like this site. I am glad that we are not academia, where every post needs to be commented a hundred times, basically turning everything into a discussion.
P.S. I have no idea why the flagger flagged the comment though, but since the question was "hot" there might have been many regular irregulars coming in for the show, trying to earn a helpful flag.