Well I'm definitely no expert, but in this month's digital edition of American Handgunner Magazine (called the September/October edition in the email), there was an article about choosing defensive ammo. If I understood correctly, the author (Dave Emory) says that in his opinion, one should seek a middle of the road weight for caliber to use in a short barrel so as to both keep velocity up but also have knock down power/penetration. He brings up that there is also a compromise between expansion and penetration and that out of short barrels, lighter bullets will be much more likely to expand fully/properly but won't penetrate as deeply, while heavier bullets will penetrate more but are less likely to fully expand out of short barrels due to lower velocity. He then leaves it up to the reader to decide whether they would prefer deep penetration or good expansion
However, one should also look carefully at the propellant being used. Several companies are now making short barrel rounds using faster burning powders that can propel heavier bullets better out of short-barreled handguns. With these types of rounds (such as Speer gold dot short barrel or buffalo bore short barrel rounds, just to name a couple of the more well known short barrel offerings), you can get enough velocity with heavier bullets out of a shorter barrel to penetrate more deeply and still expand well.
That's my two cents, but I'm sure that somebody much more knowledgeable than me in both the production of ammo and ballistics will chime in with a more detailed and thorough answer.
EDIT: oops! looks like a couple already did chime in while I was typing and reviewing my post. Serves me right for leaving in the middle for a few minutes.