Textures in Freespace work by loading a list of the textures used by that model when the ship is 'paged in' (Basically whenever the game knows it's going to be used). These are the textures from the 'textures' tab in PCS2. When you do texture replacement, it also includes the glow and shine maps. However, that texture list from the PCS2 tab is used for everything - including submodels. They just store the texture's place in that list, not the actual texture itself. So if you change that texture, you will change the subobject.
With some coding, a moderate amount, you could do per-object subobject texture replacement regardless of that list. For now, if you change a texture used by a subobject, it will change that subobject. But it'll also change any other objects that use that model.
I don't know how you'd do this, besides editing the POF file manually, but if you did add identically-named textures to the list, you could perform texture replacement for that subobject and it wouldn't affect anything else (provided the subobject was the only thing using those identically-named textures). You could probably do this by importing the POF with a separate set of textures for those subobjects you wanted to do texture replacement on, and then opening the POF in PCS2 and renaming the subobject-only textures so that they were the same as the general-ship textures. As long as you had the UV coordinates set properly, you could then toggle the glowmaps on and off for one subobject while still only using one set of textures for the whole ship.
As far as slowdown goes, I don't think that you'd experience anything noticeable by using that method, at least not until the renderer is heavily revised. Right now, FS2 renders each set of textures all at once, and then moves on to another set. That means that it first loads the base map, then the glow, spec, and normal maps. Then it moves on to the next subobject and does the same thing. So it's continually changing textures anyway. However, you will still run into the MAX_TEXTURES limit if you use too many texture sets, even if they all have the same name.
(Side note so I don't have to talk around it in the future, textures in the textures tab from PCS2 are loaded from the POF file as 'texture maps', which contain references to the base, glow, spec, normal, and height maps that've been found and loaded. Texture maps are more or less an extremely primitive precursor to some kind of material object.)