ill tell ya what, we have a 21' Bennington pontoon and it is most certainly NOT a bow fishing boat, but i took the rubber shop mats from menards and a couple tarps and covered the bottom, we took a 8' 2x4 and put 6 250 watt halogens on it and clamped it to the front, it worked but wasn't the best, we had fun though.
ANYWAYS aside from that story, if i were to do a pontoon (which i would LOVE to) I would find a cheap 16ft (depends on where you bow fish for size) pontoon from craigslist (make sure the pontoons are 16 ft not the deck) i would weld beams across the pontoons and make the deck completely cover the pontoons. i would make the front 4ft a large box baisically 2 ft high and the width of the deck. I would make the entire platform storage as well. With the rest of the boat its up to you. That is how i would do it.
depends on what kind of water your shooting. if its mostly flats a toon should work fine. I have heard that they are hard to turn if your have a front mounted troller, and if you have alot of weight in the front they get pushed around by the wind alot. I have never shot off one personally so im just going off info i have heard. I personally think that a bowfishing pontoon boat would be awesome
In response to the "hard to turn with front mounted trolling motor" yes it is kinda hard but, if its pretty calm there is no problem, we have an 80# minnkota trolling motor on the front of the 21 footer and it can move that 5500lb boat easy with no worrys of hitting a dock or bottoming it out.