I would not seal the pylon to corner casting... not that it would cause much problems - more because it will not fix the real problem for long...
Thake the frame off and check out the foam plugs... The ones in the front pylon have ventilation tubes. The rear pylons could (depends on year)have lead in them. Replace the foam if it is questionable (water noodle foam works well) - also consider taking the lead out (mine - '85 - did not have lead in the pylons).
Nylon hut with crack... I guess this is common. Replacing them with SS lock nuts might not work well since the bolt is not long enough to reach the nylon insert of the lock nut. Do not over torque what ever nut you use - IIRC this was the reason why Hobie used the nylon nut in the first place.

Patrick