Many of the ones I see being used for back bay and ocean front fishing are the sit in style. They are becoming more popular each season. We have been in several Fluke tournaments where they actually have a separate category for kayaks.
I have never used one for fishing but I think a sit-in would have more storage for gear and be a little more stable in wave action.
Sit in....sit on.....does not matter as long as you get out fishing