Michael, here's a picture of a void at the forward V berth portlight on the port side. It comes from here:
http://c34.org/bbs/index.php/topic,3241.msg17589.html#msg17589
The inner liner is separated from the exterior fiberglass. This occurred only on the aft section of the portlight, the two pieces (inner and outer) were completely connected on the forward side of the portlight. I believe this is what George was describing.
If it was my boat, and the condition pictured below is what you are finding and what George described, I would follow his advice and over drill the holes, fill with epoxy and re-drill and rebed the handrails.
If, however, you are finding soaked plywood, then you'll need to ream out the holes as far as you can and fill the cavity with epoxy and then re-drill, and rebed with sealant.
Your remaining questions are reasonable; the good news is that you are reporting that the voids seem to be like the ones shown in this picture because you can get the snake way far inside. There appears to be no reason to fill that void, your goal is to seal the holes where the screws and bolts for the handrails come through the deck to avoid any water penetration.
Where will the water go? There are no weep holes, the idea is to keep the water from getting through the top of the deck.
Laminated layers? The laminated layers mean the different sections of the deck assembly. There's the gelcoat then the fiberglass, then maybe a wood core, then more fiberglass, then sometime the void, then the headliner. Don Casey's "This Old Boat" and many other books have a much better description of how the assembly is actually built. Your goal is to determine if the intrusion is into the core or the void. I'll leave it to George to respond to what he found at his padeye.
"...the area immediately adjacent to the bolt holes should be thoroughly filled to prevent any water that does leak down the holes from weeping into the gap between the headliner and the deck mold." -- Yes, that's the idea behind "over-drilling" the holes and filling with epoxy and re-drilling for the right size bolts and screws, as described in reply #1.
On our boat, none of the holes for the handrails were "lined." The factory drilled through whatever was there and put in the bolts and screws, and in many cases the sealant was less than would be expected or that would be installed by a boat owner who was concerned about future leaks. We've re-bedded our handrails, the starboard side earlier this year, and the port side two years ago. Leaks that were detected, necessitating the re-bedding, we did not examine for core rot. I did not remove the handrails, since I found it's harder to get them back in by a complete removal than it was to just lift them up enough to clear out the old sealant below and rebed them. There has been back and forth discussion over the years about whether to remove or just to lift the handrails (the teak ones, that is) for re-bedding, and even for refinishing. Some choose to remove, I chose not to.
The newer boats may have had a beefier support and lining for the chainplates, as George described, but on my boat they sure did not. I've re-bedded my chainplates any number of times and found no "lining" there, just deck, core and liner. In the picture, it appears that there was no wood core where the port light was installed.