IMO - loose hooks are a bad idea - not just because they might migrate from one compartment to another, but what happens when you turn over the box and spill it? Last time that happened to me - the hooks were all in the packages they came in or in a small zip lock bag that I got from Michaels and it was a pretty simple matter to just pick up all the little baggies.
As many hooks as I routinely carry, I hate to think what would happen if I should spill a box and it was all filled with loose hooks. Given my eyesight, shadows and whatnot, I'm not sure that I would find them all. If I spilled it in my shop - that would be bad - I know that stray hook would find a tire at some point. If I did it at the ramp, there is a decent chance that stray hook would find some one else's tire, or toe, or child or dog toe, whatever. If I spilled it in my boat, it might find my toe, that one time I was barefoot in the boat.
As you might guess by now, I think that loose hooks in boxes are a bad idea. I would advise keeping them in original packaging or getting some 2" x 3" zip lock bags. They are pretty cheap at a crafts store, like Michaels. As far as hook organization goes, then I keep like intentioned hooks together. I use heavy duty plastic pencil holder zipper bags that I got at Walmart for less than a buck each. Sling blade Flutters go in one bag, tx rig drop shot hooks go in another, Gammy wicked wacky hooks go in a 3rd, tx rig slug & stick bait hooks go in a 4th and so on. I carry 8 ro 10 different bags and then when I inevitably spill one of the bags I don't spill all my hooks and it is an easier and safer clean up.
Regular tx rig hooks & weights (of which I carry a lot) are all packaged in a similar fashion but kept in a 3700 size, one compartment box, in the gear bin in the boat.
Hope this helps. IMO keeping loose hooks in a Plano box is just asking for it and if you spill the box away from home there is a chance you could hurt some one other than yourself.
The karma of some one else stepping on your spilled fish hook is a philosophical musing for another time . . .