It's probably the reformatting that fixed the problem, not the slow-mo. I had a sporadic problem with freezing as well but after reformatting it hasn't happened since, and no using slow-mo at all.
Think of it this way; since the save file for DIY is quite large, if the save file is fragmented it's going to be difficult for the game to save the file (especially since the game was designed to write data to a dedicated memory unit in a DS cart, not a MicroSD, so it wasn't designed to handle fragmented files). Reformatting and copying back the files essentially defrag the save file so the game saving should be a lot more stable.
Using slow-mo would help a bit since that would slow down the game-saving process and make it handle a fragmented save file better.