Stef

To answer your third question directly, because the settings screen is genuinely confusing and the labels do not mean what they look like.

Settings, then Apps, then the app, then the Siri & Search section. There are usually three switches:

• Learn from this App — feeds usage into suggestions. Turning it off does not hide the app.
• Show App in Search — whether the app itself is a search result. Off here and the app vanishes entirely, which is not your symptom.
• Show Content in Search — the app's own indexed items: a note, a conversation, a saved recipe.

The thing you are missing is not on this screen at all. There is no per-app switch for App Shortcuts. That is why toggling these has done nothing for anyone who tried it, and why every thread about this ends with somebody insisting it worked for them and nobody able to reproduce it.

So: check that Show App in Search is on, because it is worth ten seconds, and then stop looking at that screen.

The charging-and-idle detail deserves more weight than it gets. It is the difference between "this is broken" and "this has not run yet", and almost nobody controls for it before posting.

If you are the kind of person who charges from 20% during the day and unplugs at 80%, the device may genuinely never get a long idle window. I have seen a phone sit wrong for a week and sort itself out the first night it was left plugged in until morning. Before concluding anything, give it one proper night: plugged in, on wifi, screen locked, and do not pick it up at 3am.