In Windows Azure SQL Database, a database "server" is a logical concept that's used to keep details of connected databases. It does have a "master" database but it's not like the on-premises equivalent. It's pretty much a container for logins.
Generally there is no point provisioning a server that has no databases. Servers aren't charged separately, only the user databases are charged for.
The Azure team has now made a change that means that if you have a server that hasn't had any user databases within the last 90 days, it will be automatically deleted. It's important to be aware that this can happen. The only thing that would be lost would be any pre-configured logins. You would need to recreate them when you later decide to provision a user database.