Very true, I don't know why I forgot about those. Then, there actually is a decent amount of hints. Rebirth cave has to be a pretty big hint IMO, there is one part in the cave with a big pool of water/magma which almost exactly resembles the caves that Groudon/Kyogre can be caught in, in Emerald. The part with the houses on top of the water in Shizui's town reminded me of Pacifidlog straight away.
Also, the fact that a Rustboro remix was programmed into B2W2 but is not used ANYWHERE in the game could very well be some sort of evidence too. Although, I think I remember that they put a remix of Suicine's battle music in FRLG and it meant nothing but who knows.
The hints are quite subtle, because you can't be 100% sure as to whether they thought of them as hints or not when putting them in but I'd say the ones you mentioned are very interesting and its likely that they could be hints.