If there is an administrator of apex workspace and he needs to protect or lock certain applications in the workspace against some developers or users of the workspace.
Can this be achieved in current apex release?
No. Within the Builder there is no user/application access control below the workspace level: workspace developers have access to all applications within that workspace.
If No what is the workaround?
No workaround, just standard APEX practice: if it's necessary for developers to be restricted to working on certain applications, then the workspace must contain only those applications the user can work on.
At runtime, access to applications can be controlled using authentication and authorization schemes.