Good sleuthing! Just in case this may help you (and if it does apply to your boat, which I would guess it would).
When two "walls" of fiberglass or fiberglass/wood are joined together, it is often done by "tabbing." To tab (say a right angle joint), you grind/sand back a few inches on each "wall," clean it up, and then you wet out a strip of fiberglass mat or cloth (picture a strip of sheetrock tape) and then lay it in place to cover the joint. Fiberglass doesn't like to lay down over sharp bends, so often one would lay in a fillet of thickened epoxy or some other material (foam, other resin) to smooth the gap. Picture laying in a caulk bead on an inside corner before tabbing and you get the idea (or you would round over an outside corner). Working in an area like an anchor locker is cramped, and it's not always easy to be quite as perfect as you would be out in the open.
So, the "sides" of the anchor locker are the hull, the bottom is (I believe) a fiberglass or gelcoat covered piece of plywood (or if not, something with a similar function), and the aft "wall" (mini bulkhead dividing locker from v-berth) is molded fiberglass. My guess is that the tabbing that bonds the locker bottom in would be the most likely culprit. The two places I would check are where the bottom joins the bulkhead that divides the locker from the v-berth, and where the drain goes through to the outside. A tiny flaw in the tabbing in either place would be able to let water through. The only reason the drain hole is included in the equation is that it likely passes through the tabbing that holds the locker bottom to the hull side in that area. Thus if there is a little gap in the tabbing there (picture it was never laminated perfectly, which is common), then you drill through the tabbing, through the gap, and through the hull for the drain hole. Now water can pass into the gap as it drains, and thus get below the locker bottom.
Mine looked like there was not a water path, but I did investigate and work in this area because the drain hole on mine was too high. I cut a new, lower hole, made sure there was no tabbing gap (lined hole with thickened epoxy anyway), and I also laid in a fillet and a new tab on that joint between the locker bottom and the dividing bulkhead. Now I know there can be no gap, and as a side bonus it is smooth and more easily cleanable.
I believe I wrote this up with photos in two places:
1) Thread I started called "Sunbeam ~ 22 Cruiser"
2) An older thread on the anchor locker
Also there are photos in my album, some annotated. Our boats are probably not identical, but I would guess the construction in that area has not changed hugely.
Initially, I considered putting in a tube or something the drain (such as Tyboo's fuel vent solution), because I had read there was a liner there. But after investigating it, I could see the "liner" (at least on my boat) was just a bit of tabbing, so I felt a good fiberglass/epoxy job would be preferable in my case. But as often is the true, there is more than one way to do the job and have it work.
Sunbeam