In my experience Kuhli Loaches are save with shrimp. As for aerating, Kuhlis will rummage at the top for any food but I haven't noticed mine digging into the substrate. At the most they will wriggle some of the top layer loose to get under a rock or decoration to hide.
I think what is generally used for substrate aeration is trumpet snails, but I don't know if they would be good in your NPT!?
My kuhli loaches also dig into the substrate to hide. I don't think they will do what you're hoping for though as they usually do so at the edges of the tank or near decorations and plants and only until their bodies aren't visible, which is often less than 1/2 of an inch.