Unfortunately, there is not a way to add the version number in MATLAB Compiler APP. The development team has been informed about the enhancement request.
As a workaround, you can create the standalone application with the version number appended to the name of the application. For example, the application name can be myApplication_v1_0_5. This would allow multiple installations of various versions in the same system as well as have the version name in the application's shortcut.
I am sorry about the inconvenience that may cause.