How can I delete Image Capture's history of past "Scan To" folders?
Here's a workaround that just succeeded for me. 


In the Image Capture utility, open the Scan To: pop-up menu, and remember each folder in the "history list" part. Not just the name of the folder, but its parent folder.
Quit the Image Capture utility.
In Finder, rename each of the folders from the "history list" part. You don't need to delete the folders, but you do need to be sure that nothing exists at the path where each of the folders was.
Run the Image Capture utility again. Open the Scan To: pop-up menu. The history part should be empty.


Worked for me, on Mac OS X 10.11.6 El Capitan.