It depends entirely on the context. For routes where total travel time is mostly governed by moving time, and the stationary time in stops is negligible, the capacity boost from double-deckers easily outweighs the longer (un)loading times. The alternatives to increase capacity can also be problematic: with longer trains you start running out of platform length (and long platforms add walking time); while running more trains closer together requires more personnel and rolling stock, and is limited by signaling block size and braking distance.