Yes that's what I thought the first time I completed Dead Money. I ended my second DM playthrough today, and he talked about it during the conversation inside the Sierra Madre's Vault. He doesn't go into detail, he briefly mentions it. The devs put it in on purpose nonetheless.
Also: I'm not sure the BoS and the Enclave would have been able to get inside the facility. Elijah mentioned it's extremely dangerous and he almost didn't make it out alive. We only know about Elijah, Christine and presumably Ulysses gaining access to the Big Empty, and they're all pretty tough survivalists. I'm not sure the Brotherhood or the Enclave would risk losing a lot of men getting into a facility with unknown content.
The Enclave was an active group before the bombs fell, they were the proverbial "string puller" that controlled the American government, so its hard to think they couldnt have known about it before the war. Been tied up in it or something. Afterwards, when the bombs had fallen it might not have been a big concern for them, they could have forgotten about it, etc. But they (as in the pre-enclave people who eventually became the enclave) likely were involved with it.
Also, christine is not really that tough, at least in my opinion, she was a brotherhood scribe, she wasnt even a warrior. Both her and elijah were once members of the brotherhood, one is 70 years old and the other is a women, so maybe it isnt that hard to get in.
The enclave (who may at this point be destroyed anyway, from their defeat in the west and east) would have ahd the ability to get in before the events of fallout 2 when they were for all pratical purposes wiped out in the west (this is based off of avaliable information).