My commentMy comment as an answer:
Yes, it's quite fine.
The only thing I'd make sure though, is that the logo ends up being vector in the end, rather than a raster image of a 3D rendering.
Which would often mean that if you originally make it in 3D application, you'd potentially need to recreate it or at least finalize it in something like Illustrator.
Depenping on how much of a 3D look I'm going for, I would use a 3D rendering as my "guide" to recreate it in Illustrator ( Just a quick render ) or just a 3D model converted into 2D line drawing. If possible, I would use both methods together.