I tend not to use surface plugs in rough water, merely because I find them more difficult to fish. But are they less productive in choppy water than when the surface is calm?
I'm not sure if you're talking fresh or salt.
In salt water I used various plugs (primarily cedar) in some really beefy conditions. 1000+ miles offshore, tradewind belt, 4 meter seas, etc. In those conditions (trolling), the plug is mimicking a bait fish that's at the surface, occasionally popping and bubbling. I have a cedar plug with a lot of teeth marks on it, and it's provided many great meals.
In fresh water I generally get better results from something like a bucktail jig or spinner. The surface plugs don't really mimic any type of natural prey that I'm aware of (in fast moving water, skipping about the surface).
In fast moving fresh water my experience is that bottom fish need bottom fish tactics, and something more like a trout is hiding out in the river bends under the banks, looking for opportunities to go right in front of their faces. Sub-surface stuff does good for me there.