I've never tried using auctex remotely, but in general if you have a file open in Tramp, you can also run arbitrary shell commands with M-! and M-& remotely, as well as opening shell buffers that let you run commands remotely as normal.
Yeah, that's right... You could scp the .pdf back to the iPad, but that's a bit cumbersome. Oh, well, unless you give Emacs advice to do that for you after each latex command...
Edit: Clarity.