I'm another newbie like you - just got a good condition Nacra 5.2 and had water in the hulls too. Unfortunately nowhere near the little amount you had. Set it in the boat yard for a few days to let it dry out, then got under it. The Marine Tex patches put on by the previous owner looked ok but a little proding/tapping on them quickly showed where the drops of water still in the hull were located. Digging out the patch filler I found a hole of 1 inch long and almost 1/8 wide - ya get lots of water leaking in that even with the patch stuff sort of over it. Always wanted a water ballasted Nacra! I'm going to do some fiberglass work over them and seal tight and hope that solves my leak problem. Like you I too redid the hull plugs just in case.