Does an oscilloscope subtract voltages as phasors?
The math subtraction function in an oscilloscope subtracts the instantaneous values of waveform 1 from the instantaneous values of waveform 2 to create a new waveform comprising all those instantaneous subtractions. A basic (or expensive) oscilloscope does not understand phasors.

Here is a pictorial example of a noisy sinewave subtracted by a clean sinewave with the output (in pink) being just the noise: -



Picture from here.