There is a time and a place for every technique. I don't think flyfishing is an "either/or" sport unless you want it to be. There are situations where a fly fished under an indicator will do better than without, and so on. The trick is to figure out when that is. That's what makes flyfishing so much fun.

I will say that for the first ~10 or 12 years I nymph fished I never used a yarn indicator. After that, I started using an indicator a lot. Fished properly, the technique is insanely deadly, sometimes almost too easy. So I will say that an indicator will work, even in complex currents, if fished and mended properly with the correct length of tippet and weight. If you don't adjust your length and weight to every drift you won't be as successful with this technique. Personally, I've just seen way too much success with this technique to pass it off as ineffective under all but special case situations.

BTW for the type of river you described my thought is that a dropper-dry set-up would be ideal (I bet you already do this). I often fish a small nymph under a big attractor with a #6 tungsten shot about 8-10" above the fly. I'll use between 24 and 48" of fluorocarbon tippet between the dry and nymph tied to the bend of the hook on the dry. On smaller, pockety freestones I have yet to find a more effective nymphing rig. Here in Colorado on the Big Thompson, a small tumbly freestone that fishes really well at 50-200 cfs, it's my "go-to" set up. Just treat the dry like a yarn indicator that will catch more than its fair share of fish, even when there aren't any bugs on the water.