Indeed. Actually some of SotN's 3D effects pass right under your nose with you barely noticing them. It starts out quite dramatically in Richter's fight with Dracula when he assumes the 2nd form. The polygons making up the tiles of the throne room fly off into the distance to reveal a giant rotating 3D model of a vortex bearing a monochrome plasma effect texture.
Then there are little details, such as the doors between areas, the Demon familiar's wings, the Sword familiar's advanced attacks, and of course, the gigantic multi-sprite bosses who rotate their weapons and limbs perfectly (this being done simply by applying a rotation matrix to the polygons, rather than rotating the raster graphics as would have been done on Super NES). There are countless other examples, but they escape me at the moment