i was recently using mame .108 for a long time, but i got sick of MK2 having volume problems...so i updated to the latest version of mame .117. after upgrading, i only had 3 roms that didnt work anymore, so it was easy to get newer versions of just those 3. (i only run about 50 games on my cabinet, so checkign them all doesnt take that long.)
I use MALA as my front end and only run one version of mame, but you could in theory set up multiple versions and switch between them if you really wanted to.
as for the hiscores and savestates, i dont really care about that. i play the games to have fun, i dont worry about the hi scores.