Don't try to deploy these libraries as part of a normal setup.
Microsoft Scripting Runtime must be installed through the use of a
self-extracting .exe file. For versions of Scripting Runtime mentioned
at the beginning of this article, the only way to distribute it is to
use the complete self extracting .exe file located at the following
locations...
It is possible that some users employ an older anti-malware suite, many of which tried to disable scripting. It is more likely though that some users have managed to break their Windows installation, either themselves or by using applications improperly packaged to try to include these libraries - and blindly remove them from the system on uninstall (cough, cough - Inno).
The libraries involved have been tailored code for some time. This is why the ancient .CAB file was "recalled" long ago. There is no single copy of them intended to run on any random version of Windows, and there are no redist packs for any modern version of Windows. The correct fix is a system restore or repair install.
While this can't be blamed directly on InnoSetup because it is the result of poorly authored scripts it is frustrating enough and common enough that I won't cry when its signature is added to anti-malware suites. There are just too many poorly written examples loose in the wild copy/pasted by too many people.
I spend plenty of time undoing the damage caused by uninstalls of these applications and have grown quite weary of it. Where possible I use isolated assemblies now in self-defense, which helps a lot. Windows File Protection is getting better about preventing abusive action for system files too.
But in general you are much better off avoiding any dependency on scripting tools in an application. There isn't very much that they can do as well as straight code anyway, though it may take some time to write alternative logic.