It will get messier unless all of your drive bays and PCIe slots are empty (save for one boot drive and one GPU).
I admit there are probably many MP users like that, but looking at your sweet setup I am skeptical that yours would be empty inside!
Not in any appreciable way though.
My point is that MOST of my studio is outside my computer.
Certainly I have hard drives in the Mac Pro- I have two- the boot drive and the audio drive.
I also have a couple of externals for backup and archive.
The audio interface is external.
Everything else in my studio is external- keyboards, compressors, EQ's, Mic Pre's, speakers, cabling, patchbay, iloks etc.
That is all external.
One extra HD won't make a tiny bit of difference to how messy my studio is.
Mine isn't that messy though- I have everything on patchbays and can route any input to any output.
My point is though that for recording studios most of the stuff is outside the Mac Pro. One or two more things outside the box makes absolutely no difference to me.