The stanchion base may also not be the source of the leak, it may just be the exit. The C-30 is plywood cored and water travels through it quite easily and then exits where ever it can. Being that this stanchion is at a low point water could be leaking into the deck further up and just exiting at the penetrations for that stanchion.
Have you determined that there is water dripping off those particular stanchion nuts?
You may also want to check your anchor locker as they are often inadequately sealed by the factory.
Follow me here:
Water drips around the lip of the anchor locker then travels/wicks along the underside of the deck to the gap where the wiring comes into the anchor locker. Once past this bulkhead it can then track its way along the top of the hull liner, behind the trim board, and tends to drip out at the low point, as it won't go back up hill.
To rule out the anchor locker you can simply rim the anchor locker with duct tape hanging down to make a drip skirt so the water can't track on the underside of the deck. All you need is to leave it hanging down a quarter inch below the deck all the way around the locker flange. This way when water runs off the deck and into the anchor locker it tracks down the tape and falls off the bottom edge into the abyss of the anchor locker instead of tracking along the underside of the deck..
With the C-30 there are many possibilities of where that leak could be from. Oh and NEVER seal the underside of the deck only the surface side. If water does get in you want to know about it..
As Don said avoid 5200 (AKA Devil Glue). Sikaflex 291 or 3M 101 are other great alternatives with significantly lower adhesion.
Don't forget to bevel/chamfer/countersink the bolt holes when putting it all back together as this will keep the water out by giving you a nice o-ring and sufficient thickness for any movement of the fittings so as not to break the seal. The link below explains a lot about countersinking..
Drying a deck is next to impossible unless it is very localized. Usually by the time it starts to drip out, the core can't physically hold any more moisture. Eventually it will start to drip brown, like coffee, and then you have a real problem of decaying and rotting deck core..
If you find you have lots of moisture I would not "pot" the holes with epoxy as that will just seal the moisture in with no room for any to drip out. If you have a dry deck then potting the holes is a great idea but not so much with a wet one. Wet decks, to a degree, can still be structurally sound but you need to stop any further water ingress as soon as possible..
Sealing Deck Core Penetrations (LINK)