Ray, 95% of my fishing is sight-fishing on the flats (Chatham) and for 95% of that fishing I use crab flies. Late April though Early October. The only exception is tiny tuna. I use sinking lines, floaters, and intermediates, but I'm always sight-fishing. You could count on two hands the number of blind casts I make in a season. That's just my preference.
In the early season I often use an indicator, especially if I'm using small flies and clear flylines around pods of fish. With very few exceptions, I've rarely fished with anyone that easily detects that actual taking of the fly -- the opening mouth and the flare of the gills are too early to set the hook with a crab fly, and the tug on the line is too late.
Something happens in between, and I can't describe it. If you watch an indicator you will see what I mean. Most years I've found that "sixth sense" by June, can dispense with the indicator, and can just watch the fish.
I don't see your point about differences in where the fish are in the water column. Some days they won't take a crab unless it's on the bottom, other days I've had fish rise up to meet a falling fly. I've never felt the need to adjust my fishing style too much. If you're regularly hooking fish deeply on flies, in any circumstance, there's angler error involved.