I get this issue on pixel 7a, but not only "after reboot", it's much more random.
I mainly use two user profiles back and forth:
#1 is always running in the background with google play without account and no playstore.
#2 is not running in the background and has no google play services.
So far the webapp in profile 1 hasn't disappeared after two or three updates and reboots.
For profile 2 I just have to switch a bunch of times between profiles during regular use and eventually the shortcuts are gone.