Hi Marc and Welcome to the Q&A Board!
Let me make sure I understand what you're asking ....
If, for example, I set my shutter speed to 1/100 (shutter priority) and the exposure is still too bright at minimum aperture (F29), will an EV adjustment of -1 actually darken my image? Where are the adjustments being made if I'm at the limit of my aperture range in shutter priority mode?
Super duper question Marc!
I've found that on my camera, the exposure settings (shutter speed and f-stop) are listed as remaining the same as does the ISO value. (This info was obtained from the EXIF data for the test images.) The images, however, do darken as I adjust the EV from 0 to -5. So in answer to one part of your question, YES, adjusting EV does affect the final exposure even when at the limit of aperture range (at least on my camera). Take a few test pix on your camera and see if it does likewise.
But what is the camera actually doing? Got me! I'm really intrigued! I suspect it's magic

but I'll put in a query to the Nikon Tech Support and see what they say. I'll post their reply when I hear back.
Cheers!