I'm not sure what you're looking for here.
The application does things like "if you delete an issue, remove all the custom field, comments and history data for the issue".
I think it might be useful to know why you're asking about referential integrity?
There are lots of places where JIRA chooses not to make the DB data consistent. For example when you delete a filter, gadgets that were using the filter display "Filter not found", but the DB config for that gadget still refers to the deleted row in the searchrequests table. Or when you uninstall an add-on that provides a new custom field type, then reinstall the add-on, the data was never deleted.
But I do think that something like the Integrity Checker that scans for these cases and cleans up the JIRA data would be very useful in the long term
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