Leopard smart folders

A smart folder really isn't an alias, it is a query that looks like a folder, for lack of a better explanation. That query has to be saved somewhere and when you delete the folder you are, in effect, deleting the query as well.

Not sure what the problem is here. I tried to duplicate your issue but found this instead:

Duplicated a document on my desktop and gave it a unique name.

Created a new smart folder, specifying the new document as the search parameter.

It found the one document, and then I hit the save button. The default place to save was in Saved Searches (which is a folder in youraccount/Library/. I also let it add the smart folder to the sidebar.

Then I opened a finder window, navigated to myaccount/Library/Saved Searches, and dragged the smart folder to the trash. Emptied the trash. So the smart folder is gone.

The document that was the only hit in my example was still sitting peacefully on my desktop. That is, trashing the smart folder did NOT trash the original files, and certainly should not. A smart folder is simply a saved search that automatically updates it's search results when you click on it. The things it finds are not actually in there, and deleting the smart folder should have no impact at all on the found documents.