Happened fairly regularly where I worked, maybe once per month. Normally just transmitted clearance in the blind, and never got too worked up over it. As said, completely different from someone who showed up on the runway without talking to approach or anyone else. Had the old light guns which were useless more than a mile away in daylight.
Did have one chap hauling checks who lost electrical system 200 miles out one night and forged on, no lights/radios/transponder or IFR clearance. About an hour after midnight, I cleared a DEA/Customs plane for TO and he replied "What about this Cessna on final" I about jumped out of my skin. No radar target, (very old radar on very old tower display), no lights, not visible to me in any way, but the pilots could see him from the threshold about to cross the fence. They followed him to the ramp and gave him a "special" welcome. Don't think he'll repeat that decision.