I'll tip jigging raps with a wax worm or a couple spikes on the treble but rarely tip the chubby darters. I feel the effectiveness of the darters comes from the slow, wobbling decent, and by adding meat to the hooks, it reduces that action the lure was designed to produce. Having said that, I typically only use the chubby darters when the fish are active or I am on a school of bigger fish and don't want to waste time catching smaller fish. Tipping a jigging rap will also reduce the intended action of the lure but not nearly as much as tipping a chubby darter, IMO. Very rarely do I tip raps when fishing for walleyes, whitebass, or crappies, and I still manage to catch a few randomly roaming perch on the bare raps when targeting those other fish.
My advice, lower your rap or darter down the hole to a depth where you can still see it and experiment with different jigging motions and watch what type of action they induce. That way you have a feel for what your bait is doing when fishing deeper water when you cannot sight fish and you can more easily nail down a jigging cadence that is producing bites.