What it came down to for me is that as much as I like the consistency of forcing the compiler to use something, it probably isn't ideal to make it use a short all the time if its compiling for 32-bit. I first started with the approach of, if it doesn't matter I'll just use int and I'll leave uint16_t and uint32_t for when I want to force it one way under both 16-bit/32-bit. That worked. Then I thought why use stdint.h at all, I can always use short or long to force an exact size if I need to with both DOS/WIN32.
I agree with you though that outside of that, stdint.h and _t vars make sense and could be a good thing. I guess defining the scope of what you intend some code to support from the beginning helps.