The Plano waterproof boxes are awesome and they do have them in different sizes. I decided to opt for the smaller unit for 1, 3, and 5/0 hooks. If you wanted a huge assortment of hooks you could certainly do that too.
Here's the box and a piece of packing foam. (not styrofoam)

I used an x-acto knife to cut the foam to size. Just eyeball it, it will fit snugly once you squish it in.

Gently remove the foam block and use it as a guide to cut a piece of adhesive foam sheet (99 cents at Michaels). Trim the corners of the foam sheet so they are slightly rounded to better fit in the box.

Insert the foam block back into the box then apply the adhesive backed foam sheet on top, carefully lining it up so it all fits nicely.

Layout your hooks to visualize how many you want and where they will go. Once you decide how many you want, start cutting deep slits into the foam. Use some something as a guide to make sure they are evenly spaced.. I used a small piece of foam I cut as a spacer to ensure the hooks were the same distance apart.

I thought I was finished at this point, but I decided to make a strap for it to hook to the yak.

I carefully drilled a 3/8in hole in the outer flange. Start with a small pilot hole and work your way up.

Find a very heavy duty rubber band or some sort and thread it though the hole and tighten it down.

Finally attach it to your yak! I clipped it to the mod pod on my OK, but you could hang it anywhere really.

You could create any size, shape, layout you want. I'm looking forward to having hooks handy and dry on my future trips.
Tight lines!