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.
Trains can run fully automated today, and if you are running into capacity issues they should be. You may still need more personnel, but it is a different type of personnel and full automation gives enough other advantages as to be worth it.
If the size of your blocks are an issue, then that is a problem worth solving. If you are can't fit in all those trains, then you need to build more track not try to compromise. Yes track is expensive, but if you can't fit all the trains then the passenger volume is high enough to support it. This likely requires better operations though and some people see a loss of their direct train and don't see how a fast (fast is critical!) transfer is overall better for them.
