I actually happen to have answered a very similar question on Startups Meta just the other day.
In essence, I'd say that, yes, if you're invested in improving the site and you have the will-power and desire to write a comment explaining the problem, then that's good practice. 99% of the time, unless it's a recurring problem, a moderator will not be so kind (logically so--when dealing with a hundred flags, it's difficult to stop and write something poetic for each and every one) as to leave a comment.
That said, no, it is certainly not necessary to comment. Assuming the flag warrants deletion of the post, your comment will likely be deleted as well. Sometimes I think it can be nice when you flag something as Very Low Quality, to leave a comment for reviewers to (try and--no guarantee) make sure they look specifically for what you saw, but don't trust moderators to see your comment. If your comment is necessary to validate the flag, use the "Other" option, or reconsider whether what you're flagging is truly in need of moderator attention.
In many cases where a comment and flag are necessary, the post will wind up in the "Very Low Quality Review Queue" anyway. If that's the case, it will likely receive template comments from various users there, and I generally just wait for those to come, rather than writing my own undoubtedly less concise or complete version of the same thing.