I traded up to a IXB in mid1940 and haven't had any problems with the boat. It is a touch slower, and I've had terrible luck against air patrols (read my crazy gibraltar thread), but the boat has performed just fine against convoys and patrols into early 1941. I think the key is, as in any sub, to avoid being detected in the first place. Or if you are running in hot areas, run with decks partly submerged. Your extra fuel lets you make up for the loss compared to a VII, and you can submerge just as fast (if not faster) when you're doing that.
I do plan to eventually switch back to a 41-C when they become available, but for now and until 1942-3, I plan to make the most of the boatload (literally) of torpedos I have!