From help :
EnableApplicationFiles: Applications can be imported/indexed.
Go to Help > Documentation > Appendix > Hidden preferences
There are links “On” / “Off” behind each hidden preference.
Clicking “On” behind EnableApplicationFiles should disable skipping of application files.
Offtopic: I wrote a script that indexes a duplicate of DEVONthink’s help. You can find it here Index DEVONthink help.