The last thought in the minds of the Irish parties (north and south) negotiating the GFA was any possible consequences for the UK’s EU membership. The fact of EU membership was generally recognised as a lubricant in the process: but implications beyond Ireland were not the business of the negotiations. They were complicated and delicate enough without having to introduce extra-Irish/UK considerations.
I’m absolutely certain you’re correct, which is why I’m sure the GFA can survive adapting to the new situation, and a new proposal already seems to be received well by the Irish: the customs border being the sea. Naturally, it’s the Orange who will be more likely to object.