'Yak fisher here, although relatively new to it. I bought a sit-in style, not through any belief that it was a better design for fishing but because that's the type I'm familiar with and enjoy paddling. Now that my biases are out of the way...
Sit on: A little higher out of the water, can help if you're trying to eyeball structure through the water surface glare (the higher the better). Can offer more comfort - dangle your legs over the sides and relax! Mounting extra gear (rod holders, etc) requires a little more care as any holes drilled will need to be sealed properly. Probably more challenging to mount a fish finder, at least if you're wanting to mount the transducer inside (shoot-through-the-hull). Easier to store and get at your gear for the most part.
Sit in: For me, the main advantage is stability. Very low center of gravity, comfortable and easy to control. I drilled holes for a rod holder and fish finder display with no real concern since the holes are nowhere near the waterline and don't impact any seals. I epoxied the fish finder transducer inside on the base and it works very well - will likely require a re-epoxy every couple of seasons, we'll see how it goes. Being able to use a skirt is a definite advantage if you fish in waters that can get choppy. My 'yak weighs 36 pounds (probably more like 46 with anchor and gear inside) which makes it easy to portage with (and put on the roof of the truck.)
The best advice I can give is - try both! Find what feels comfortable, and don't limit yourself to "angler" kayaks - anything you need for fishing can be added with a drill and a little care. Unless you're planning on also taking the kayak on multi-day expeditions I'd recommend a shorter model. While the sleek ones are great for paddling long distances, they're not easy to turn. With a shorter style you might not want to paddle as far, but maneuvering around that piece of structure on the bottom will be a whole lot easier.
If you're planning on drilling holes, make sure you ask if the material is suitable! I'm pretty sure most 'yak materials are, but better safe than sorry.