Update: Nintendo has responded to IGN about the differences noticed in some games having cloud save backup and others not.
Part of the reasoning, Nintendo’s official statement explains, is “to ensure fair play” in relation to online games.
Nintendo’s full statement provided to IGN reads:
The vast majority of Nintendo Switch games will support Save Data Cloud backup. However, in certain games this feature would make it possible to, for example, regain items that had been traded to other players, or revert to a higher online multiplayer ranking that had been lost. To ensure fair play, Save Data Cloud backup may not be enabled for such games.