I've got a stain in my kayak that I can't explain, so I feel your pain and paranoia.

Define what you mean by 'fiberglass,' that's just the reinforcing fabric. Epoxy is the coating which should have completely and permanently saturated the fabric. Epoxy is waterproof. The only possibility is a hole in this coating allowing the wood core to absorb water.
If you've got a really old 'yak, more than 20 years, with polyester resin--which in fact was not quite waterproof. The problem with old 'resin' fiberglass boats wasn't water absorption, but pitting and pin holes that allow water to seep in. Usually this blisters the skin allowing water in just that area to seep in. (Van Dorn Oceanography and Seamanship has a good discussion of this problem.)
I've heard a lot of sad stories of the frustrations of owning a resin/fiberglass boat in the 1970s. Boat ownership especially varnished wood and resin fiberglass, I think used to be considered one of the clear signs of middle aged male insanity. Epoxy has changed all that. Now a boat has to be over 30' to be used in court as proof of insanity.

My overweight wooden kayak seems to have gained weight over the years as well. But, even with my suspected water stain and lots of wear and tear, I don't think any of it is from water retention ( I tell people it's her thyroid not my misuse of epoxy resin.) When I've made repairs on exposed wood, I find it'll dry completely a couple of days after being in the ocean. If your kayak was soaking up water you'd probably have a mold problem that would smell bad.