Personally, I definitely think we should strive to NOT create new versions in the database as much as possible. First of all, even if the author is not around anymore, it is not fair to release a custom with our name if we're only doing modifications or additions on top of someone else's work, which is still most part of it. Yes, we can give credits to the original author, but it's not good enough. Second, we end up having multiple entries in the database, with users wondering which one they should download.
I think the moderators are capable of modifying a custom's database entry, so if the original author really isn't responding and hasn't been around for years, we should get in touch with a moderator and discuss a possible update of that custom. But then, I think we should still do it only if there is a positive consensus from the community.
I am quite sure that if we make additions to a custom (the common missing parts are pitched vocals, pro keys, harmonies, venues and reductions) everyone will agree it is a positive thing, and it's always beneficial to share them!
If we make corrections to obvious errors, that is also probably going to be appreciated.
But if we make revisions of some charts, either because we believe that a certain track doesn't properly represent what the real instrument is doing, or because we want to improve the gameplay, then things get more fuzzy... whether it's a change for good or bad will always be subjective, so I'd say we need to seek for consensus from at least someone else in the community. Initiate a discussion on the custom's page or start a thread about it.
I think I share your feelings overall, because many times I've downloaded a custom and been disappointed that the drums chart really doesn't match what the real drummer is doing, or because the guitar chart is insanely more difficult than playing the song on a real guitar (having been a guitarist myself, I know I am biased). Having learned how to make customs, I have been fixing this sort of stuff for my own use, but how do I know whether others are fine with the current chart or they would appreciate my "fixes"?
The only way is to talk about it in the forums, and see if you can get at least a few other persons to back you up. If nobody responds or backs you up, perhaps one possibility is to share your "version" by posting an external link to it in the custom's page, and describe what you changed. Maybe people will try it directly and like it.