I’m wondering why when indexing a drive DT will ask me to locate a particular app (which typically is not living on my drive.)
You are indexing an entire drive?
The message is not caused by DEVONthink. When you have a document in your database that is associated with app that OS X cannot locate, then OS X asks where the app is. This can happen when a file extension has been assigned by OS X to “open with” a program that was later on uninstalled. Locate the file that’s causing the message to pop up, select it in Finder, use the File > Get Info command, modify the “Open With” assignment in that panel, and choose “Change All”.
You’re probably indexing some AppleScript scripts which use these applications.