Probably true, but it doesn't seem like it would be that hard to allow save transfers, and you'd think Nintendo would want to encourage people paying them twice for the same game even if it's not that common.
True, they would benefit from people paying twice... but they wouldn't be benefiting from encouraging second-hand sales, which is exactly what allowing save transfers would do since there'd be no reason not to just sell the game card afterwards.
StreetPass data saves to the SD card regardless, so if someone is really willing to re-buy the game just so they won't have to change cards for easy StreetPass accessibility, it would work to Nintendo's benefit not to support game save data transfer, because those people would always be able to use the downloaded copy to access their StreetPass data, but would still have to keep their original card if they wanted to keep their saved game.
Nintendo would be getting the double sale regardless, but only if they let the save data transfer would they be more likely to lose another new sale entirely by making it easier to find used copies resold.