Custom fields created post-installation, those that do not have a namespace, are counted normally towards that object's limit. As an example, let's say you have managed fields on a standard object A and a managed object B. Your managed fields on A do not count towards that object's total field limit. Similarly, your managed custom fields on B do not count towards B's limit. However, if an administrator creates fields on B after installation, those fields do count towards B's field limit. For example, if B has 100 custom fields, and your organization limit is 500 fields per object, then B can still have 500 custom fields defined on it after it's been installed. If a package upgrade includes more fields later, they will also not count towards the limit during the upgrade process, so installation can't fail even if the maximum limit has already been reached.