sql server active active configuration with same database names I have a SQL Server 2008 Enterprice in a clustered environment and in active-active mode.

By active-active mode i mean that both instances are active and serving requests to their databases. 

Instance 1 has databases Db_A and Db_B and instance 2 has databases Db_C and Db_D. 

I would now like to create a new database called Db_E on each instance. They will have different content and structure, but will have the same name. 

I tried it and it's possible but i'm not sure what will happen in the case of failover when i shut down Instance 1?

I guess it should be okay, but i'd like a confirmation.
You have two different clusters sharing the nodes, both clusters in having one active and one passive node. The names and resources on each cluster are completely independent from the names and resources on the other cluster. So you can safely add Dnb_E and each cluster. On failover the node running now the active node of both clusters will start OK, since the Db_E on the cluster A is different from Db_E on cluster B. Notice that I intentionally avoided using the name 'instance'.

Using the misleading 'active-active' nomenclature just leads down the thinking that you somehow share resources between the two clusters. Calling this configuration 'active-active' is strongly discouraged.