Running later versions of those files will not ruin your MAME or ROMs, IF we are only talking about frontend usage.
If we are talking about auditing however, then yeah, you really only want to use the correct versions (like for like) of those files. Otherwise you can, and probably will destroy your romset. This is why you see so many of us repeat ourselves over and over again, that even if you are thinking of manipulating your romset, then make a copy first. If you destroy a copy, no tears
But if you strictly are talking about a database driven, query type of environment where these files are not altered at all (like GameEx) the only consequence really, is that some information will be incorrect, some command(line)s might be outdated, and some roms won't show up in the official list. But nothing will happen to your MAME.exe or your roms using GameEx
EDIT - And if it's your MAME version versus your rom version that you are worried about, the worst that can happen is your MAME won't run them. That's another reason why we say "make sure your MAME matches your romset" over and over again