From what I can gather from the schedules published on the MTA website, both the B and N are currently running 10 tph out of Brooklyn. The N running out of Astoria is augmented by short runs to the City Hall lower level (last passenger stop Canal St). I would assume that these short runs would be terminated with both the W and N servicing Astoria.
As I remember the B terminated at Queensboro Plaza, the last time it ran up Broadway. I suspect that one reason it is being extended to Ditmars is that the current policy regarding emptying relaying trains was not in effect at that time.
Any delays at Ditmars will be due to inability to turn trains around. The delay will be the same, whether the trains are using 2 or 3 tracks south of the station. I suspect that they are trying to save 1 trainset by running express.