They might keep SJU-STL, but I'm not too sure for how long, if at all. Yes it is a hub, but so is MIA, DFW, and ORD, and the already have multiple flights to those. I'm thinking they might use STL more for mainland traffic but who knows?
As for the LAX route, TWA wasn't doing that great with that route. They were actually getting subsidized by the Puerto Rican government to fly that route in order to give Puerto Rico more direct access to the US west coast. However, I doubt AA is going to get any help and they'll probably just axe it and keep their present SJU-DFW-LAX flight.