For me, this habit came not from Windows, but from the days of System 6.
It is definitely true that OS X manages a disk better than previous operating systems and makes formatting and defragmentation less necessary than on Windows or pre-OS X Mac OS. I do use Disk Utility on a regular basis to repair anything that may have gone wrong with the hard drive (this actually occurs more frequently than some OS X users would lead you to believe, as it's happened to every OS X computer I've owned except my new MacBook Air). Using OnyX is good too, but in some cases it won't cure all problems.
Yes, it's possible to just create a new user account, but I'd rather have a complete refresh. Call me old-school, but I like to restore my disks to their original state and rid my computer of any extraneous clutter in the process while fixing potential problems with the actual drive. We're talking about drive rot here, not OS rot (which OS X doesn't suffer from to the degree Windows does).
I agree this takes plenty of time and effort, but in the end you rid your drive of potential disk-related problems and make a nice backup of your drive in the process. Remember, too, that each case is different from machine to machine and while alternatives to formatting often will work, starting at square one never hurts.