It makes them money and people willingly pay for it. If anything from a business perspective there's absolutely no reason for it to be free.
For how stuff nintendo's servers are it better be
Nintendo's servers are typically used for matchmaking only with the actual gameplay being P2P (Peer-to-peer). Anyway the bigger problem lies in with the lack of voice chat, text chat, invites, parties, etc. Embarrassingly basic stuff that even the original Xbox in 2002 had.