Timestamps have the property of being easily comparable; you can always tell if one file is older then the other. If you were to use hashes for the same purpose, you'd have to keep a database of expected hashes, and comparing them would be a less trivial task, etc. It's doable, but it would be a very differently designed (and much more computationally expensive) program then make.

I bet we could get pretty far with symlinks, but then again even those were an exotic feature on some of make's supported platforms. Nowadays, may as well use sqlite.