I just noticed this today using iTunes 7.6, but I do not know how long this "situation" has existed.
As far as I've always known, when you delete a track from a playlist using AppleScript, the track is removed from the playlist; when you delete a track from library playlist 1 (the Main library), the track is removed entirely from iTunes. In both cases, the track's file remained in its location in the Music folder. Today I noticed that when doing a delete from library playlist 1, the track was not only removed from iTunes but its file was moved to the Trash! I could not figure out a way to keep the file from doing so. I tried deleting it from its Master Library--in this case the "Music" playlist--but it still went to the Trash. Deleting from a simple playlist worked as expected: the track was removed from the playlist but remained in the Master Library.
Recently, some users of Make Bookmarkable wondered where their tracks went and it turns out they were moved to the Trash. Not so bad, since the bookmarkable copy was re-added (I believe). Still, this is not the behavior I expect when using delete. And until recently this wasn't the behavior anyway.
If this is how delete works now, then there is no way to remove a track from iTunes via AppleScript and subsequently keep its file, which is an option when you manually delete a track using the Delete key.
So, what's up with that?