Is caulk acceptable for filling nail holes in baseboard?
Caulk is a bad choice, because it can't be sanded.  You can't get it perfectly even with the flat surface, because it stick to everything it touches.  You will end up with a slightly raised area around the hole, and it will show more readily than putty, because caulk has such a different consistency. And, yes, caulk will shrink just like putty, but unlike putty, you can't put a second coat on.