My own experience, from living in completely different geographical areas with similar length commutes (~12 miles), one with appreciable hills, one without, is that I was measurably faster, on average, on the commute with hills. My surmise was that the net effect of hills, over time, was to improve my conditioning (hand-in-hand with my average effort) and hence my average speed. BTW, the hilly commute was at an elevation over 4000' higher than the flat one. Both were relatively free-flowing rides and I would say the minor delays from the few traffic lights and other impediments was pretty much a wash, between the two cases. The hilly, high elevation commute came first, so it is not a matter of my conditioning improving over time. And I sure hope like hell it isn't an indication that my fitness is going to hell in a handbasket as I age!