I have seen the same thing. You are correct it happens when updates are downloaded on Google play apps. It happens on my phone also. I have checked my settings but found no solution.
This may be happening when the apps autoupdate, I haven't seen it enough though to carefully correlate one with the other.
I don't auto-update; I update by hand. And after I update an app from Google Play, I have to re-add it to the home page. I haven't had any updated from the B&N store, so I don't know about those.
I've seen this happen on rare occasion on my mobile phone (Android 4.0.4 ICS), but most of the time the apps stay put on the screens after updating.
I have 3 android phones of various vintages in my household, 2 older nook colors running JB on n2a cards, and a Samsung Galaxy Tab 2 7.0. This problem doesn't happen on any of those devices after loads of updates, etc. Only on the Nook HD+. I love a good deal, but the HD+ is starting to be a pain with these quirks that keep popping up after having it for only a couple weeks.
This is a HD issue.
Since Google Play Store Apps are treated differently it seems the code that handles app updates forgets to re-add App Icon to home page when it uninstalls the app and updates it.
So it happens like this:
App uninstalls. App icon removed.
New version of App installs. App icon is added back.
For Nook Apps: Works fine.
For Google Play Store Apps: The last step (app icon is added back) was perhaps forgotten when coding.
I have this happen to books as well. Since those are not uninstalling there has to be another issue I think.