Breaking it down, is there really an issue here?
I have recently found a user on Stack Overflow who has two profiles (separate issue - flagged)
There is no problem having multiple accounts (I personally have a sock puppet account) - the only time this becomes an issue is when the user uses the accounts to interact (vote, comment, answer, etc.) with each other. If they are kept separate then there is no issue. So unless the moderator can find evidence of this interaction and that interaction is causing a reputation points gain (or is being used to work around the limitations/boundaries of the site) then you can expect your flag to be declined.
asked over 20 questions cumulatively regarding the same project, getting step-by-step help asking for copy and paste code, thus making him a help vampire
Asking for step-by-step help is not bad. In fact, it can show that the user is making progress and is thinking about their questions (because they are not throwing 20 questions into one question). What really matters is the quality of the questions - are they well asked and explained, are they likely to help others in the future?
If the questions are individually okay then how you deal with this type of user is largely a personal issue.
If the questions are not of a good quality then you already have the appropriate tools at your disposal - you can edit the question, make suggestions via the comments, and downvote or vote to close if necessary. If a user accumulates enough negative feedback from the community then the system automatically actions it, no moderator intervention is necessary.
Is it acceptable to comment on all of the new questions related to the issue to inform other users of the issue?
You should craft your comment in such a way that it helps the user rather than worrying about warning the other members.