I have duck feet too! I ALWAYS have problems finding running shoes that don't give me pinky toe blisters. I had that problem with hiking boots also, until I got a pair of Garmonts (which I highly recommend if you're ever in the market for hiking boots).
I've found that Shimano shoes tend to have a wider toe box than the other brands my LBS carries (Specialized and Adidas, I think). I have two different Shimano models, and one is definitely a little wider through the forefoot than the other, so it might depend on the particular shoe model also.
Lots of people use MTB pedals on road bikes. My riding partner has Speedplay Frogs on both of her bikes. I ride SPDs on the MTB and Look Keos on the road bike, but only because I have problems with numb toes after a couple of hours on the SPDs. The larger platform of the Looks keeps my feet much happier.
2010 Scott Speedster Limited/Bontrager Inform RL
2008 Cannondale Rush 2 Feminine/Terry Butterfly
2005 Cannondale F400/Terry Butterfly