The product states in the bottom left corner that I have 2 server licenses (3 in use) - how can that be?
Click Help | About.
Ensure Product Information is to the front.
Click view/change product license.
you will see the information there.
Note that the numbers of servers configured is calculated on the SQL Server instances only, that are currently enabled. All the other connection types (Windows, VMWare, Replication, Analysis Services, SQL Azure and High Availability) are excluded from the number.
The message you see is a "friendly prompt" only and won't prevent Spotlight to connect.