Don’t worry about losing your configuration with an edition upgrade. Assuming you’re upgrading within the same version, an edition upgrade - or downgrade, for that matter - should be entirely transparent.
Ehm… With Enterprise Edition you get the ability to configure the number of workers. How many you configure is entirely up to you and should depend on your resources, as outlined in the docs
Not sure I understand the question. SonarQube is built to handle hundreds or thousands of projects in the same instance.