Good point.
(I bet they didn't want to emulate the Ram pack? No Super FX chip games either. Or it could be some bizzare Nintendo logic where they want to hold back the games with teh special chipz for future download services).
Actually, if they couldn't release it due to the Expansion Pak, Majora's Mask would not have been rereleased. In any case, it is interesting that SimCity and the Donkey Kong Country trilogy were removed specifically. The only times previously when a game was removed from the Virtual Console were due to rights issues. Irem imploded in on itself when led to their games being removed, and Konami and Ubisoft lost the Teenage Mutant Ninja Turtles license to, err, THQ though given THQ's current financial state, that may not be for long.
Donkey Kong Country and SimCity do have potential rights issues though, namely trademark issues. Nintendo does have to license out Rare's trademark from Microsoft to use Rare's logo for the DKC games, and Nintendo does have to license out EA's trademark on SimCity to use its name. Naturally, Microsoft wouldn't help a competitor and the rumors seems to have EA being angry at Nintendo for not using Origin for the Wii U.
Basically, there is every reason to believe that Microsoft and EA are just not playing ball with Nintendo anymore, and that's why the games they can affect are being removed from the service.