That boat looks like it is in very nice condition and I doubt you have any serious problems with it. My interpretation is that you were able to smooth out that ugly looking repair and you can simply cover it with bottom paint. As for the anchor locker, it looks a little small to me for your boat, but that may not be an issue. It seems that the bottom comes to a point, almost like an inverted pyramid. The first picture (with the daylight showing) seemed to show a flat bottom, but now I can see that it is more or less a bulkhead separating the locker from the v-berth. With all the dirt on the walls of the locker, it is difficult to see the condition of everything. It would help to see it cleaned off. I can't imagine that you have any real damage on those walls. The daylight looks like it comes from the inverted point of the pyramid ... therefore, I assume that there is a drainage hose leading to the clam shell, which is on the stbd topside. Perhaps the light is bright enough to follow the hose, or the opening is in a relatively direct angle with the sun.
You should be able to verify all of these suppositions. Plug the drain, fill the locker with water and watch for any sign of a leak underneath the v-berth. It will certainly follow the centerline, so if there is a leak, it will be very easy to detect. Then, when you unplug the drain inside the locker, if there is just a trickle of water, you may need to clear the hose with a flexible wire or something that will clean it. Obviously, you don't want to puncture anything you can't see. You should have a healthy flow of water out that drain. The stain you see under the clam shell could be from a slow trickle because the drains is clogged with mud ... a very common occurrance.
There is no reason to worry about the stains, I think. I guess it is very odd that it seems to be a sort of soft caulk material (you indicate it is flexible?). That doesn't make any sense to me. Anyway, your locker needs to drain and it is perfectly ok for water to come in at the chain opening and exit at the drain. That would be normal, except that you would have to be out in some really uncomfortable weather to see waves coming over the bow regularly!

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That limber hole underneath the v-berth is necessary so as not to trap water. I think it is insurance against water entering at stanchion bolts or the hull to deck joint and needing an exit. I wouldn't worry about the stain if you can clean it off. It is probably a very rare occasion that water finds its way into that void in front of that bulkhead.