Think you are right; can't find shortcalls in the application database?
If you look at the AgentPerformanceStat database there is an item ShortCallsAnswered with description: The total number of local Contact Center Manager calls, ACD calls, NACD calls, SIP voice calls, local multimedia contacts, and incoming NSBR calls accepted that have a talk time less than the short call threshold assigned to the threshold class for the skillset.
So for that AgentPerformance item altering a Threshold Class will have infuence.
Setting the Short call perimeter for an Application will have no influence since it is not logged in the database, hence custom reporting will not solve that.