The only issue, for us and webtrees, has been related to the flag poles, not the flags themselves. Google maps deprecated that option sometime ago. Or at least I assume that’s the problem you are referring to? There was a brief discussion, and a much longer debate in the wt bug list about it.
There has also been a discussion about flags today on wt, but that was just a user who forgot to copy his flag files across when moving to a new server.