Personally, I have never used InputBox(), instead using KixForms. We deploy/register the DLL to be able to use Kix to run system-service type code via NSSM.exe. Since it's there, we leverage it for the one user-based interface app.

WshShortCut is used only in the install logic of our software - one call during the install and a second that runs daily to create the startup link if it's missing.

We do use WshPipe pretty extensively, with nearly 150 references across 36 of our applications. The team here has been looking at building an EXE or DLL that we could invoke that would replicate the ability to capture STDOUT/STDERR. We also have modified WSHPIPE pretty extensively to allow more control over returning either or both streams, control the wait time, and whether we terminate the app or not after the wait time expires.
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Actually I am a Rocket Scientist! \:D