check iTunes Preferences, the Advanced tab, the settings for “iTunes Media folder location” and “Keep iTunes Media folder organized“.
If you have your iTunes library configured to keep everything under a preferred folder location and to let iTunes automatically organize the items in the library, then deleting an item should provide a prompt asking whether the item should be moved to the Trash or kept in the media folder.
I recently noticed that iTunes wasn’t prompting to move deleted items to the trash anymore (resulting in left over cruft taking up disk space). After checking several things, I found the preference settings had been lost. After correcting (restoring) the settings iTunes did prompt to organize the folders and appeared to do a quick scan thru the media there (a couple minutes), but it finished quickly and everything seems to have returned to normal.
*I can only guess the setting problem cropped up a couple days ago when I had some problems with external USB devices and had to forcefully disconnect and shut everything down.
iTunes version 11.0.1 (12) on OS X Mountain Lion 10.8.2 iTunes Media Library is location on an external 1.5TB USB3 HDD. I’ve been using external storage for iTunes for about 4 years now, so that of itself wasn’t the source of the problem.