To elaborate slightly on what Jyrki set and to answer point-by-point:
How to flag abusive comments that may not look abusive at first sight?
For the flag select "in need for moderator intervention" instead. Once selected you will get a window in which you can enter explanatory text.
When in doubt if a flag is clear without explanation and context, go for this option. As mentioned by Jyrki a moderator might well only see the flagged comment when deciding. I think it does not change all that much for moderators work-wise especially if you keep the explanation to the point. In principle a "rude or abusive" flag can lead to auto-deletion, but it also feeds the moderators' flag queue so that often also this flag will result in moderator intervention.
Is getting a lot of declination harm my profile (like temporarily locked, blocked from flagging etc).
There is something like being banned from flagging or being warned before flagging based on ones recent flagging history. But, this for flags on posts (not comments) and the worst possible thing is that you cannot flag for a few days. See Rule for getting banned from flagging for details.
A declined flag here or there, especially on a comment is harmless. It should also be noted that for a comment flags it can be tricky to avoid declining a flag even when it is justified. Basically a moderators is faced with the following alternatives: either delete the comment or decline the flag.
Thus in a case where a flag has merit but the comment that got flagged should not be deleted, there is no way but to decline (except if one is willing to trick the system, by deleting and undeleting, but that's tedious to do for comments and not really a good option). Also, on comment flags moderators cannot give feedback. Thus, if the situation in a comment thread is convoluted, it can be better to flag the post (not a comment) for moderator intervention.
That is to say, a comment flag can even get decline without explanation, even when a moderator agrees with you.
If so, please someone look into it, it was literally a helpful flag!
While you were already reassured by a moderator that indeed your flag was correct, do not expect a change of the flag-status itself. Again, this is impossible.
To sum up, while persistent poor flagging could have consequences, don't worry about a decline here or there. If the problematic situation persists after the decline, and you are pretty sure it was just a lack of information or a misunderstanding, flag again and explain the situation.