The tool considers a non-interactive running environment when the output window is set hidden, and so it suppresses these internally handled user interaction methods.
Anyway, you may use any other object methods, such as the
WshShell.PopUp one.
You may also create a library script in VBScript language, to declare message and input help functions that use the language MsgBox and InputBox methods, include that library in your jscript script (check
this post on how to do that) and call these methods from your script.