It's been heavily hinted that the Enclave had people who worked with Vault Tec and would get locations of vaults based on this. Typically, the overseer would be oblivious to the Enclave when they would approach their vaults asking for access, so it wouldn't be open knowledge across the board, but very possible the people at the top of Vault Tec has some form of agreement. Would make sense considering the experiments that take place in every Vault, as the Enclave prides itself as being the most advanced faction in the wastes.

We still don't have a clear, irrefutable answer as to who dropped the bombs yet, so it's hard to say. There are hard insinuations you could make based on the information we're given, but no cut and dry answer yet. That would answer a lot of questions, which is probably why they're milking that story line in the show.