I would not be to concerned about the deck issue as it sounds localized. I would suggest that you have 2 options. 1. Take the wait and see approach. If area does not get any larger, then no worries. 2. Do some exploratory surgery. (I personally would do number 2 as I would just be too curious.) I would explore by drilling thru upper skin and core, but not thru lower skin with 1/2" dia drill. This would allow a visual inspection. If core is wet then you need to find source of water intrusion and stop it. If core is dry, then filling hole with very runny epoxy will very locally rebond. Good luck and I would be curious how you proceed.
-Jeff-