Is it OK to copy (not clone) a git repository using basic Unix commands?

It is perfectly fine.

git stores all of its history, commits, etc. on site - this is a fundamental property of a DCVS.

Technically speaking, git can operate just fine with copied repositories running around everywhere, because the whole point of a DCVS is that it doesn't have to know what's going on outside of any given repository, and in fact doesn't unless you tell it.

The same principle applies here.

You should be able to copy the entire working directory to anywhere else on your system and have it continue to function as normal when using Git, Hg, or SVN. I can't comment on other SCMs.