You've made an interesting point there, but I'd say why not both? I think science and magic can easily co-exist, Nicodemus was a sorcerer after all, we do see him magically pull his staff towards him after all. Perhaps Nicodemus unlike the other rats gained not just far greater knowledge but also came to possess his magical powers, which he gained from science when they were changed in the lab of NIMH. As for the amulet, who knows how it came to be but I don't think it really matters, I love this film, it's my all-time favourite film.