The game didn't come out until October, so it's possible that there was a cut off date. Games like RE4 came out in their respective years during the spring, and by the summer, had likely sold millions of copies. So maybe that's a potential reason for why it has been omitted.
Such a shame, though. Comeback of the year / decade, and one that restored my faith in Konami again. It will likely still take home at least one of the other awards. 'Best Audio' or whatever, and 'Best Acted', etc.