One cylinder of my two-stroke bike (e.g. Honda NSR250 MC21) misfires at low rpm. Is it the ECU?

It may not be only the ECU. Before replacing it, check the other possible causes (plug caps, coils, pickups, carburation, power valves). If the original ECU is confirmed faulty, Ignitech offers a DCCDIP2 race unit with a plug-and-play connector adapter for this bike.