When creating a new copy of a database with File -> Database -> New Copy, there is an option to only copy the design and no documents from the source database.
When creating a new replica of a database with File -> Replication -> New Replica, there is no option like this. The replica stub that is created will not include any documents, but it will not allow administrators to make any modifications to the database design or the Access Control List (ACL).
To create a replica of a database without any documents do the following
[via Lotus Notes Knowledgebase # 1097325]