I am looking into buying a used hobie 16, though one i am looking at has a couple very small cracks where the hulls connect to the tramp(i dont really know what this part is called...) Does this mean anything is wrong with the structual integrity of the boat? and if so is it easily and cheaply remedied?
Depends on the cracks. I think you're talking about tiny cracks in the deck around the pylons? If they appear to just be cosmetic it's probably okay. If it looks like they go deeper then you might have some issues down the road. I guess that's pretty generic advice but it's the best I can do with the detail provided. 
could i like put some epoxy or something like that on it to just make sure it doesnt like spread or get any deeper or anything?
If the cracks are annular (circles around the pylons - the aluminum part that comes out of the hull), that's a dead giveaway that the pylon has come loose in the hull.
It's repairable, but it's a lot of work. Depending on the age of the boat, it might be better to pass on buying it.
Cosmetic cracks in the gel coat are no big deal.