If I put 100 IntValues into my character from a script, will the game lag or crash?

No, this won't lag / crash. It will take a short time (maybe 60 milliseconds?) when you create them.

But objects that you can't see pretty much cost nothing to just lie around.

Changing objects takes time. Creating objects takes a bit more time. Destroying objects takes time, too. Reading from objects takes a little time.

By "a little time" I mean a millisecond or so. By "a bit more" I mean a few milliseconds.

That means it's okay as long as you don't do it constantly.

This is only true if the number of things made stops at a reasonable count (say, before 500).

That said, there's probably not a good reason to keep that many objects (you shouldn't have names for all of them, for sure).

Consider using simple tables to keep track of data instead.