I have not heard about Nintendo stealing away purchased items; I would assume refunds would happen and in some places (like my state) it's unlikely they'd go against the law.
Reusing a game key doesn't prove anything more is going on; however, it doesn't prove otherwise. We simply do not know if they have 100s of these things hammering their servers in various ways - they wouldn't report that. We also don't know if they've done really stupid things that makes it a possible risk or if they unjustifiably view it as a risk. Well, knowing security, you assume the server is not secure - you can't prove it is secure but you can prove it is not secure with 1 breach. We have mitigating policies built upon theoretical failures that may never happen. This could be such a policy - do I agree with it? no. I'm just arguing it's not "clearly an act of evil."
evil---
Overly broad definitions ruin the purpose of the word and in this case, actually help real evil by conflating it with lesser instances, accidents, mentally ill acts, thoughtlessness, etc. The serious problem is how situations get humans to do horrible acts; when humans often do not act like they have free will...