Should separate Drupal installations have separate temporary directories?
They can all share the same folder if you want them to, but if you want to give each domain it's own tmp folder that's fine too...it really depends on how you want to set your server up. 

Aside from being able to identify which tmp files have come from which site (which personally I've found no need to do up to this point in my life) I can't think of an argument either way to be honest.

Edit: Thinking about it a bit more, if you're running a shared host of any description it might make sense to provide a tmp folder for each domain so it's sandboxed from other sites, and from the main system tmp folder (and subsequently other parts of the system that don't relate to web).