I was messing around today, loading up a ton of saves until I reached the brick limit. When I pressed the Clear all bricks button I wondered if the command /brickcount would still count the bricks while they were being deleted, I tried it and INSTANTLY every single brick was cleared.
Try typing /brickcount in the chat after you hit clear all bricks. (I tried this in single player)
I am guessing its a glitch or something....I dont understand why deleting the bricks take so long normally now.