Same issue here.
I wrote the details of my configuration in my previous topic on how to deal with a large library. Initially, I just wanted to get some advice, and then the time issue showed up.
I deleted all the Engine folders on C:\ and E:, I reformated M:
I add with drag n drop the E:\Musique folder to Collection, and wait several hours the full indexation and analysis of my library.
This morning, with this fresh install, “aggregating drives” still took 19 min 
CPU is at 20%, RAM at 80%, disk usage looks low.
Nothing shows up in event viewer.
I recorded a video, but I’m not sure that it helps.
Oh! And I’m running Engine DJ 4.3.0, of course.
The performance of my SSD external drive are quite good. And in fact, during the “drive aggregation”, Engine DJ is essentially consuming CPU with low I/O on drives.
I would say there is something wrong in Engine DJ code.
Similar tasks in Virtual DJ: batch / add to search DB (from root music folder) takes 44 seconds, then Database / remove missing files from search DB takes less than 5 seconds (same drive, same library, of course).