I haven't heard of any specialty hoods, but I do know that my Campy Athena hoods are very wide and flat and comfy. My Shimano brake-only hoods are very narrow with a nice offset so I'm not weighbearing on that joint at all, and they are also very comfy.
Two ends of the hood spectrum, and both feel great to me. I used to have a lot of trouble with that joint in both thumbs, so I do try to be careful. Splints and thumb exercises made a huge difference for my left thumb, but my right is still fussy sometimes. My thumbs love me more when the bars are rotated up and the hoods are nearly horizontal and even with the forward curve of the bar. (so the whole top section is flat: bars and hoods)
Maybe go to a shop and ride on a few bikes with different hoods?
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