It works for the GB/GBC (--> MBC 1-5, which are nothing else than Mappers as far as I understand it... anyone correct me when I'm wrong), so why shouldn't it work for NES?
Only problem is that there are hundreds of NES Mappers (okay, only a handful of them are really important...) and I don't think that developing a Flash System would be worth the effort commercially (e.g. for a company like Bung).
-- Matthias