From the expert on all things NTM/mycobacteria (a snipping from his research paper, Dr. Joseph Falkinham). Bottomline - YES - we can use humidifiers safely. Choose evaporative humidifiers.

"Room-Size Humidifiers. Small, room-size humidifiers can generate aerosols with high numbers of NTM; even from reservoir water containing relatively low numbers of NTM (500 CFU/mL). In particular, the new ultrasonic humidifiers generate a high density aerosol mist that are rich in NTM (Hamilton and Falkinham, 2018). If you need to humidify your air (especially during winter), only use a room evaporative humidifier. Evaporative humidifiers boil water and the mist is blown by a fan or simply rises. Boiling will kill any NTM or bacterial cells and thereby be relatively free of NTM. The ultrasonic humidifiers do not heat the water, but use ultrasonic vibration to produce aerosol droplets. If a room-size humidifier blows water through a wetted filter (called an evaporative humidifier), don’t use it as the water wetting the filter will have NTM that can be aerosolized.

Remember that NTM will grow in biofilms in the humidifier’s water reservoir. Therefore, scrub the surface of the reservoir before refilling to reduce the number of NTM and other waterborne pathogens in the biofilm. I suggest you use a bathroom scrubbing agent. You can even disinfect the reservoir by adding Clorox® (1 cup to 10 cups water) for 30 min. Then be sure to rinse repeatedly until you can’t smell the chlorine before use."