IIRC Symphony of the Night is actually 3D as 2D, on both PS1 Saturn, so I doubt the PC FX could handle it at all.
This...makes little sense, I'm afraid.
There is nothing in the game's core logic - the physics, the collision detection, the AI - that would have necessitated or even had any use for a Z-axis. The same goes for the vast majority of the graphics. Only a tiny number of objects and effects, like the clock tower at the very beginning of the game, use what might be described as real 3D. These things would be mostly impossible on the PC-FX, it's true, but they're just ornaments. If anything, the developers probably had do extra work to adapt those objects to work in the main 2D engine.
You might have heard that the Playstation does all 2D as 3D because it slaps 2D graphics onto 3D polygons and displays everything from one locked perspective. This is kind of true. I don't know, I'm not a programmer and I'm not deeply familiar with the hardware. I'm guessing, though, that this only makes a very superficial difference in the way a 2D Playstation game is processed, e.g. that you have to add some perfunctory Z-axis coordinates but not actually do any math with them.
Anyway, 3D is not the reason why the PC-FX would have trouble doing a close conversion of Symphony of the Night. Lack of rotation and scaling support in the graphics hardware is.
Was there ever a 3D add on planned for the FX?
Yep. They had a chip lined up and everything. There was a board they released for PCs called the PC-FXGA that was aimed at hobbyists, and it actually had the chip in addition to the rest of the PC-FX hardware. Here is a video of the demo game that came with it.
