Whether or not water can enter the core material depends largely on where the water is coming in. If it's leaking in under the frame installations, or from another place on deck and appearing at your overhead
hatch, then core exposure is certainly possible. If it's leaking in between the lid and frame, then core exposure isn't so likely.
When we bought Jo Beth, the overhead
hatches wouldn't seal as the gasket (it appeared to be original) had collapsed. There was a gap between the gasket and frame of both
hatches which was wide enough to slide a greeting card through. Remarkably, they never leaked. When we replaced them with new Bomar's, the old frames were still well bedded and the surrounding areas of deck structure solid as the day it was built.
Last year, I had a bizarre incident. We were secured in our slip and had been through a series of gales, all with heavy, heavy rain. Early on a Sunday morning, I was sitting at the saloon table when a gust of wind heeled us over. A steady stream of crystal clear water peed forth from the overhead saloon
hatch - for a solid thirty seconds. It has never done it again; I haven't been able to replicate it with a water hose; it hasn't happened in subsequent storms (two tropical storms included - Alberto and Beryl); and I can find no reason or cause for it.
FWIW, I've not heard of this as being a common issue with PS boats.