Is my guess correct?
Most likely, considering a mod has confirmed. We have to take the mod’s word at this; no non-diamond users can see deleted comments (there is no priviledge level that unlocks it).
Is this a standard practice?
Yes. To quote from the help centre:
You must specify a reason for each comment flag. The most common cases are listed in the comment flag dialog box:
- rude or offensive
- not constructive / off-topic — a comment that does not try to improve the post it appears on, or which introduces a topic unrelated to the question or answer
- obsolete — a comment that is no longer relevant because it has been addressed by an edit to the post, clarified by additional comments, or contains no context because it references deleted content
- too chatty — anything that's not relevant to the question or answer
Thus, if you commented and the content of your comment has been edited into the post, your comment became obsolete and should be flagged for deletion. Last year’s Winterbash even had a hat for that.
What comments are eligible for deletion?
Every comment. ‘Comments are temporary “Post-It” notes’ (source: help centre), i.e. every comment should be removed once it served its purpose (or if it never had a purpose).
However, we do like a bit of fun, so the highly-upvoted joke comments often stay around as long as they do no harm.
should I flag such comments whenever I come across one?
Yes. Any comment which requests edits or criticises things that have since been addressed in the post in question can (and should) be flagged for deletion. That is what the obsolete flag is for. Since it is sometimes quite a lot of work for mods to determine whether something is obsolete (or so I was told by a mod at Chemistry.SE), you may also choose to leave a custom flag quickly stating why.
The same thing goes for comments saying ‘thanks!’ or ‘great answer!’ — that’s what voting and accepting is for.
Do I get to be mentioned in the answer? It's my content after all.
In an academic world with a strict peer-reviewing system you would. But here, it’s at the discreetion of the post owner to cite you or not if they include your suggestion.
The difference is that in academia you actually get reputation for being cited. Here, you get reputation for votes on your post. If you suggest an improvement to a different person’s answer, you are doing that out of philanthropy — effectively allowing someone else to gain reputation faster. The Stack Exchange code does not search through posts looking for @somebody sequences, does not ping you if you are mentioned and does not give you any benefit.