I doubt seriously that a z-scale nail head would be visible to the naked eye.
How high should it be to match a z-scale flat car or boxcar sill? That's the critical dimension. Of course, you'd have to take into account the rail that's 2' high...
True, the nailheads are ordinarily not visible, but they make a nice effect. Like using bricks or ballast that's slightly larger than it should be to add visible texture.
In addition to "two-foot high rail," one must also take excess ride height into account. It's worse in Z than N, I believe, so thinking about it might make your head explode. (winks)
I'm looking at starting to correct ride height in all of my Z scale rolling stock. It will of course affect coupler height, so it's not going to be an easy fix by any means, especially since I don't have any handy power tools like a small milling machine.
Oh, if you're using ordinary sectional track, like Marklin's, the distance from datum to the bottom of a freight car door is ~0.30 inches. I dont know what it would be using M-T roadbed track.