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There's no one way to tell whether an app is in used. An app could be doing all sorts of things, which you would have to track in different ways.
For example:
- App provides workflow functions: Search for uses of the functions by going through the workflows (My own Adaptavist wrote a free utility for that actually - Microscope is intended for admins to prepare for a Cloud migration, but it does it by identifying workflow functions)
- App provides new field types: Read the list of custom fields and look for the new types
- App provides new gadgets: You'll need to read a database table to see the app identifier
- App provides new reports: These often don't write anything usable into the database, you'll only be able to discover these by setting up and using access logging on the web-server or proxy
- And so-on
So, you can see there's no single way to see the usage of an app.
Zephyr has quite a footprint (fields, gadgets and reports), so it should be easy to spot, but the easiest way to know what projects use it is probably to go via the fields it adds. I would
- find all the fields that come from Zephyr(as per fields in the list above)
- create a new search for "<zephyr field 1> is not empty" and save it
- Go to a dashboard, and add a filter statistics gadget, which uses your new search, and groups by "project"
- The gadget will now show you how much that field has been used in a list of projects
- Edit the filter to search for the next zephyr field and refresh the dashboard
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