I think that is a spendid way to store hooks, Normand. (Seeing as how I do something similar - patting us both on the back!)

My wife bought me an inexpensive carrying case at Michaels (or similar craft store) that was filled with plastic boxes, very similar to your pill boxes. I label one box on it's side as "dry fly", another as "wet fly", a 3rd as "streamer", and so on. These boxes fit sidewise in the carrying case, so when I unzipper the case I can immediately see the specific box I may want.

Then, I label each compartment within the case with the hook style and size, going from left to right across the box with the hook sizes in sequence.

You'd be amazed at how many tens of thousands of hooks you can carry in such a small space, yet be able to put your fingur on exactly the right hook within seconds.