There was a time, on Android custom roms, if you had pirated apps installed, they were uninstalled automatically. I see something similar happening here.
I'm sure Apple will do malware scans on third party apps, like they do on the Mac. But if they start uninstalling legitimate third party apps, that's going to be treated as "no allowing third party app stores" and the maximum EU fine for that is high enough to bankrupt Apple. They won't do it.