There's also the fact that while the link cable was a direct 1 to 1 connection, with wireless you could have like 10 people all trying to do link cable multiplayer at the same time and Nintendo would have to do some additional work to get a way for you to choose which person to connect to and have the game recognise that.Just guessing, but it might be a case of latency. Wireless latency can be unpredictable and must be accounted for in netcode. I bet the link cables expected perfect synchronization—when they didn't get it, the link code threw up its hands and died.
Now that doesn't sound like it would be all that hard to do, but you know how much Nintendo likes modifying their roms.