Ah, the hubris of a Frankenstein! Actually, I would think it's quite possible to manhandle the database directly, as you suggest. In fact, what else could the nodetype module be doing, but performing some database surgery that one could also perform manually?

I don't know what the SQL commands would be; I expect that dissecting the nodetype module would yield clues. I've got too much on my to-do list, so for now will stick to letting nodetype do the heavy gravedigging for me. But who knows, maybe some night when the moon is full and the Van de Graaf spheres are crackling, it'd be illuminating to strap down a node and take scalpel in hand...