I like the magnet idea!
I would go for the drain at the lowest point in the locker (obviously, as that is where I put mine), because I don't like any drain water sitting there, if I can help it. I don't see any point in raising the locker floor, as that's also a project, and so I'd figure one might as well just make sure there is no void in the tabbing (or repair the void if there is one). Then you end up with the deepest possible locker and with no "mystery things" buried under an epoxy pour (or whatever you raise the locker with).
I'm probably repeating myself here, but here is what I found:
1) The way the locker is formed is to put a triangle of plywood in to make the bottom, and then to lay glass (or mat or something) over it and then tab that (i.e. use strips of fiberglass and resin) to the hull sides and to the divider between the locker and the V-berth. So picture a separate bottom piece, and then "tape strips" (the tabbing) running around the edges.
2) Now picture that those "tape strips" are made of such a material that they don't like to take tight corners (which is how fiberglass is). So where they make the ~90º bend from locker bottom to locker sides, they make a radiused curve instead of a square/flat corner. Now picture trying to get that all to lie flat while you work in the cramped bow with sticky fiberglass. The "voids" occur where the "tape" did not quite lie flat on the "wall" after going around the corner. So then when you (or they) drill the hole for the drain, it goes through the inside tape layer, then through the void (if there is one), and then through the other hull. Water of course "finds" the void and hence drains down into the area below the locker.
So here is what I did (my locker had a drain, but it was too high up and would have allowed water to stand). I figured out the lowest possible point (after port corner) and drilled the hole. Then I looked VERY closely to see if there was any void between the tabbing and the hull. In my case there didn't appear to be one. If there had been, I would have closed it off. I did still "paint" the inside of the hole with slightly thickened epoxy, just to coat the edges and fill any micro voids. Then I mounted a slightly larger clamshell, but that's because it would cover both holes (the too-high one and the new one); you won't have that problem, so could go with the "normal" sized one. In my album for the anchor locker I show the normal and jumbo sized ones in the same photo with a standard utility knife, so that would give you an idea of the sizes.
I considered doing what some folks have done, which is using a fuel vent that has a nipple (which then lines the hole). But I figured I would want to put that in with thickened epoxy to fill any void (had there been one) and so why not just epoxy the void and not need the vent tube thingie. Not that it's not a valid alternate approach.
Sunbeam