The Spirit thing is a sore spot for a lot of people because they believe they're just like trophies and there should be no reason they should deconfirm in their minds. People don't want Spirits to be deconfirmations because then they have to accept basically every Nintendo character and a handful of third parties (Shantae, Rayman) are off the table. And that's very dire if your most wanted is in that spot, because it's not a "hard" deconfirmation but it would mean you will spend months wondering and then possibly end up with nothing.
They should have probably made Shantae an Assist Trophy like Shovel Knight. At least she'd get a spiffy 3D model and the fans would be able to say their demand was at least acknowledged (not that the Spirit isn't already an acknowledgment, but again, some people don't take it as a hard deconfirm).