I think the answer with a core is don't drill, unless you really have to.
I haven't experienced balsa dissolving, but I definitely have seen it happen with ply.
But I chose neither- I put foam in my cores. I don't put much stock in Pascoe's article. If what he said were true, then my Divinycel would have cost less than the OSB I laid down in the pickup to protect it for the haul back from Merton's.
I would avoid a 2000 and later boat unless you understand what corners might have been cut on the later boats. There are also a bunch of guys on the Cape who can look at a boat for you.