Using Keyboard Maestro you can automate emptying DEVONthink’s trash including dismissing the confirmation dialog. For this create a new Keyboard Maestro macro with the following steps:
1. Type Shift-Command-Delete.
2. Pause for 0.25 seconds.
3. Press the OK button.
4. Execute some AppleScript code to empty the Finder’s trash.
5. Post a Growl notification.
If you like the idea of automating things, you should have a look at Keyboard Maestro.