Keepit sums up all used Salesforce and Salesforce Platform licenses across all connected Salesforce environments irrespective if the same user exists in multiple environments. The type of Salesforce environment (production or sandbox) does not matter.  

Important: Keepit will also back up the data of deactivated users.

The number of used licenses can be found in the company information section of Salesforce setup (Setup > Company Settings > Company Information). 

Example: Keepit is connected to a production and a sandbox environment.  
The company information section of the production environment shows the following numbers: 

The seat count will be 800 + 100 = 900 seats for the production environment. The sandbox has the same number of active users as the production environment after a refresh, so the total seat count is 1800 plus any additional users created in the sandbox environment for instance developers, trainers or testers. 

When 100 Salesforce users are deactivated and a refresh of the Sandbox has taken place after deactivating, the total seat count will be 1600, but Keepit will still backup the data of 100 deactivated users across the two environments.