It all depends on how you have them set up, if you have them in the 'classic' position, intended primarily for use from the drops, the hoods shouldn't matter, because you aren't going to be riding in them.
If you like a position that's more of a compromise, and you mount the hoods in a higher position (but not so high as to compromise braking from the drops) it can get a little awkward. I've found I like the angle of the hoods, but it might take a bit of getting used to.
I'll post a pic of my bike later (although it has command shifters at the moment), the idea still stands