this is not surprising. When a game that has to be balanced is bieng tested some maps and weapons get rejected as unbalanced that may later be rebalanced and introduced. most gamers do not see it, but often you have 3 rejected maps for 1 that makes it to the game, all in the name of balanced competition. and weapon balance is almost always a point of contention, maybe Nintendo is just being careful here.
Changes and alterations in the name of balance can be made without locking content from those who've purchased it.
Sometimes it can, sometimes it cant. For example World of Tanks took out around a dozen maps that were unbalanced and brought them back in after a rebalance around a year later. had they left those maps in for that year, people would have to play on unbalanced maps for entire year while the developers get their shit together (seriously Wargaming is very slow on updating anything). There is also very good reason not to leave overpowered weapons in a game until you balance them, otherwise peoples enjoyment would suffer.
Im not saying that this is necessarily what happened in this case, but this stuff happens in game development all the time and with good reasons. Of course the smart thing to do for nintendo here would be to simply not have the content on the disc. but discs are printed months in advance and testing and balancing is still being done until release. It may have been too late.