Yes, you can exclude devices. If you have a scenario where you know you won't deploy third-party updates to certain devices, departments, divisions, etc. those endpoints can be excluded from your licensed device count.

We ask that you calculate your device count based on the devices that will receive third party updates to the best of your ability.

A few examples of excluding devices could be:

Excluding servers, if they will not receive third third-party software updates or application from our service.
Mission-critical devices that can't receive third-party updates or applications.
Excluding departments that aren't applicable 
Mac devices
Linux devices