Personally, I prefer option number "b". Like Chris said, the knuckles lign up better with the bones in your forearm for much better transmission of energy. When performing atemi with a closed fist, I use this method of striking (Probably because I've studied Wing Chun as well).
Odd as it is though, when practicing techniques against a punch in Aikido we usually defend against a punch performed like option "a", where the wrist is rotated to allow the knuckles to be horizontal with the floor. I've had the opportunity to train at different dojo around the country, and I've found this style of punch to be pretty common.
I'm not sure which is better for Aikido training (at least from a defensive perspective), but I do believe that option "b" is better for atemi. Have a good day!