It is profitable to play with a small stack because there are two built in advantages that large stacks simply don't have. Both involve multi way pots.
1.) The second best made hand (big stack) may blow a good draw (also a big stack) off a hand he would have won with. Have you had a big stack, the draw would have (probably correctly) stayed in. Big lost pots become small won pots this way.
Edit: This is not foolproof or obvious. It becomes fool proof if a big stack folds the best made hand.
2.) Big stack play looser against each other. Example: You raise, a fish with a big stack calls. Another big stack calls with a marginal hand, because of the presence of the fish. You have, on average, higher equity than normally due to this. The big stack might think twice before risking his stack versus you. Now your presence is just a little bit annoying to him.
These advantages are always there with a small stack. There are no inherent downsides (built in -EV spots) with a small stacks.
I never play myself with a small stack, an I personally think that 100BB is to shallow for good poker on all streets. The only time I'd consider playing with a small stack is when playing a stake I don't belong playing in.
If those are the objective points, then if you are a good player, you should have higher EV playing with a full stack. Contradiction? No, the best EV would be to move up in stakes, and play with a small stack again.
There are other values to playing than EV. Everybody should sooner or later learn how to master deep stack play.
/Johan =