Why does the application in focus hang for several seconds when a drive spins up?
I know exactly what you mean
Mine does it with my external HD

It drives me nuts.
I've replaced my HD in my MBP with a SSD.
I've been thinking about replacing the SuperDrive with a hard drive tray and putting the original drive in it, but if my computer is going to hang to spin up the HHD it isn't worth it.

I guess I just have to buy one, install it, and see what happens.
I'll let you know Tuesday when the caddy tray arrives if it is an OS-HD issue, or a OS-USB issue