I would just like to point out that retexturing the base nude textures may not produce the results you want as I believe those textures are shared by most of the nude meshes, male and female, so you will get some weirdness in things like the romance cutscenes. As for the problem of the textures not showing up, not sure what could be causing that. Maybe the nude mod had the vanilla basenude textures included and is therefore not referencing your new ones?
From what I could tell, the male texture is on the top and the female on the bottom. I was only trying to edit the female, but you bring up a good point on romance scenes. I didn't even think of that. Maybe I can at least tweak the texture to make it a little more detailed.
Are there absolutely no changes at all? Or maybe faint changes? The only thing I can think of is you need to make the alpha white in the areas you edit to make changes on skin textures show up properly. Beyond that I don't know... are you still able to replace other textures?
EDIT:
This makes more sense. Have you tried changing your armour to the nude mesh with Cheat Engine (without having the nude mod applied).
Also I agree that changing the nude textures probably won't give you what you're looking for. The game applies subsurface scattering to skin textures to make it seem fleshy and realistic. If there's a way to turn this off, I haven't found it (followers have special mask textures which turn it off in certain areas) but there isn't anything like that for the Inquisitor.
If you do find a way around it, I'd love to know myself.
I didn't even think of the alpha. After looking around, I figured it was whatever applies the skin tone covering up the base texture, so the alpha makes sense. Right now, there is no change at all. I used the flycam to zoom in pretty close, and saw nothing. I had 'arm' and 'torso' written across it in huge letters, so something should have been visible.
I also didn't consider subsurface scattering...might be best to just give up on clothing that route then.