That would be nifty, though the actual 3D model's design is going to be highly debated as to how they would approach her
Actually, now that I think about it, it will absolutely be Half-Genie Hero art because that's the art already used for both Shantae and Risky in the base game, and it just makes sense to maintain consistency. New fighter spirit art can probably still happen, though, and they can use the Shantae GBC cover remake used for the Virtual Console release if the original art is too old.
As for how Shantae will look in 3D, I'm hoping the design is closer to Risky's Revenge, a little bit of Pirate's Curse. I'm personally not the biggest fan of the art direction after Pirate's Curse, and I think Risky's Revenge is her best look officially.
The remade GBC cover art nails it too, but what also nails it is the Shantae art used for Indivisible, the best 3rd party interpretation of her in my opinion.
To be honest, though, it's extremely hard to envision Shantae in 3D because it just hasn't been done yet. There are fan works, yes, but none of the attempts I've seen hit the mark. Even when they're going for the most recent art style, there's always something very off. If she gets into Smash, seeing her in 3D will be the most exciting thing about her reveal.