Spotlight on macOS gathers information about apps wherever they reside and the App Store app consumes that information to decide which apps have updates available.
Make a backup of the apps in question. Then try tampering with the app contents in a targeted manner:
- Using Finder, right click the app icon and choose show package contents.
- Locate a folder named _MASReceipt and delete it.
This removes the receipt that tells the App Store to manage the app and addresses the update bubble. Whether the modified app still runs is the next thing to check.
In many cases, this wrecks the app since it’s now been tampered with
The long term answer is to have the developer code sign their app in a manner that lets you opt out of upgrades or provide a signed / notarized version of older apps when there is a legitimate need for some people to stop updating the app. It costs them time and money to ship apps, so I find approaching them with a budget helps to get this extra work if you really need support for past versions of apps.