I believe it to be because of intonation issues. The thickness and nature of the plain metal B string knocks the intonation very slightly off, resulting in the string sounding slightly sharper when fretted compared to the five other strings. The notch corrects this, making the vibrating length of the string slightly longer, fixing the slight sharpness experienced when fretting (this can be adjusted more accurately on an electric: when intonating, play a twelfth fret and harmonic, and if there is a difference in sound, it needs to be fixed).
If the notch wasn't there, the B string would sound 'out of tune' compared to the others, making chords sound more out of tune than they should.
Hope this helps!