In question 2.2 of the lecture notes on Semi Conductors - Basic Principles, the effective mass of electron holes in the valence band is found to be negative. However, shouldn’t we use E_{vb,h}=-E_{vb,e}? This would yield a positive effective mass for electron holes in the valence band. Or is the given E_{vb} already for holes?
That energy is already given for holes, yes. You can see how the more holes you have, or the more momentum holes have, you get less energy (more negative energy). Which is the opposite that would happen with electrons so it makes sense 
If you plot the bands you can also see how they are the typical ones for direct semiconductor near the fermi energy where you expect to have negative hole mass.