Having archived applications on MacOS. How to tell OS to ignore them?
The easiest way is to zip each one. Right-click and select "Compress Name.app" (where Name is the name of the app).

Then delete the app. If you want to restore it, just double click on the zip file, and the app will get re-created.

Other possibilities include putting them inside a disk image, and then unmounting it.

Any method in which the app is no longer available to the OS will work. Otherwise, if the OS can 'see' the app, then it will be considered as viable and integral.