StrEIT, I believe it is just ignored.
For one, the difference between the maximum and average shear stress for a wide flange is much less than the 1.5 for rectangles. My Salmon and Johnson, 4th edition, has an example on page 392 showing the maximum shear stress on the wide flange in the example is 18.1 ksi. The average shear stress, using V/(d tw), is 16.0 ksi, a difference of 11.6%.
We do wind up with less factor of safety against shear than we normally have for other checks, for the three reasons mentioned:
1. Using the average shear stress.
2. Using 0.6 instead of 0.577.
3. Phi is 1 instead of 0.9.