I haven't done a direct comparison but used to use the below flip out type on my DII condenser set up.

I never noticed image degradation but I guess it has to happen. Whether it shows in the print is the main issue and I was quite happy with up to 11x14 (largest I did then). My filters were in decent shape.

I later went to above the lens and I'm now using a Dichroic diffusion head. The diffusion head definitely isn't as crisp as my below lens period so I think it all comes out in the wash

I wouldn't sweat using below lens filters if you are happy with your prints. I doubt you'd gain much.