There are two properties on the Application object to help with access control.
If you toggle on the 'Encrypt' property, the saved Application will be encrypted when saved to a .jmpapp file, a data table, or add-in (any saved form that runs the application). This encryption is equivalent to Edit>Encrypt Script for a JSL script. Note that the .jmpappsource file, which opens into the JMP Application Builder, is NOT encrypted. This is the "source file" and the developer must keep it safe.
Optionally, you can set the 'Run Password' on an encrypted Application. This password would be needed to run the saved encrypted application, but again is NOT needed to reopen the .jmpappsource file in App Builder. There is no concept of a login name - only the single password is supported.