I'm not sure, but my gut reaction is the same is yours, a hollow glass liquid-filled tube in an ultrasonic bath seems like the potential for problems. You might want to look into a thermocouple thermometer, or at least be sure your thermometer is alcohol filled instead of mercury. Also, the thermometer should be in a vessel with the sample, not the bath. Still, I wouldn't leave the thermometer in place, I'd just check intermittently.