I completed this game several times on my N64. At the 'THE END' screen yes, the console locks up and you have to reset. When I re-loaded my file I started at the entrance to Ganon's castle because the game does not save in any way after you beat Ganon. So don't worry, your emulator/ROM is behaving exactly as the original game did.
Personally, I think the not-being-able-to-save-after-the-ending-credits thing is a homage to more retro games, where you had to switch on, play, and beat the final boss all in one session and then you switched it off.
About MM - I bought a special Zelda edition of NOM a while ago, and in it they said they actual considered MM their favourite Zelda game of them all. Contraversial!