What hinges are cheap and durable? They will be used for a storage hatch on a small jon boat

There's no doubt you could go a cheaper route but I would go with a piano or continuous type hinge. Aluminum or stainless (preferably stainless) for material.

Boat compartment hinges take a lot of abuse. 

Brass or Stainless (preferable stainless) piano hinge, but they may be fit the cheap part of the equation.

I just saw piano hinges at Home Depot yesterday. 

Whatever you choose be sure it is made from metals that don't rust; brass, some grades of stainless steel and aluminum. Piano hinge is both small width and stronge. Your boat may not be wide enough to add lockers with hatches.

Get yourself  11" X 17", 1/4" grid paper and layout your boats inside shape with measured dimensions and add the compartments on paper before going any further with your plans. A good scale is 1" = 1'.

Tom

Check to see if you have a local boat junk yard.  You can buy the hinges and pulls off a junk boat.  That's what I'm doing for my next project.