I need to plan capacity for Novalys SQL Server Repositories.
If I have 5,000 users for a large application, how large should I expect the Repository size to increase?

The number of users is not the only criteria to determine the size of the repository.
This size also depends on the number of applications, Permissions and Roles you will declare.
It also depends on your auditing strategy (the more events you log, the larger the repository).
As for user accounts only, you can expect the repository size to increase by 10 to 20 MB if you create 5000 user accounts.

Does your 10 to 20 MB number include the auditing information?

yes it does. You can expect ~5MB of log for 5000 users created