What possible data can I lose if I backup iPhone to iTunes and then restore? I heard that restoring iOS could eliminate the Other category bloating problem. But I'm very OCD about all my data and have a lot of apps. Also I know that iTunes don't backup apps anymore (even with the old iTunes with app support I think only small percent of apps, presumably old apps, were actually backed up as files for me).

I know I should create encrypted manual backup cause I want to keep the passwords. I suppose that if some of my apps were removed from the App Store to the point of not being accessible in the Purchased section, I will lose them, right? Is there no way to know other than checking all my apps in store one by one?

Have you experienced losing other specific data (app data, iOS settings, etc) when restoring via iTunes?

I can't stand that after clearing gigabytes of data, the system still warns me about "not enough space". Or when it downloads 2gb of iOS 12 without asking and then warns about not enough space. Or when I remove that update, and it says that I have only 1gb available (wut).
But I want to be prepared for what comes, cause I really hate having reinstalling OS'es and losing data in the process, just cause I wanted everything to work properly.
What is not included in the iTunes backup itself:


Media (synced with iTunes but not in the backup). Videos, music, podcasts, etc.
Books (can be synced with iCloud or exported with third-party iTunes replacer if stored locally). Includes both ePub and PDF stored in iBooks app.
Apps that are no longer on the AppStore and not accessible via Purchased > Not on this phone (as you've already mentioned). But app
data is still saved in the backup and can be accessed with
third-party apps.
App data of some apps. App developers decide what to include in the backup, so be careful with messengers like Viber or Signal (they
can have a separate backup way, check google), or with important
docs. Media players usually don't include tracks/videos as well.
Some data that is synced with iCloud. For example, if you have iCloud Photo Library with "Optimize storage" enabled, iTunes backup
will include only thumbnails of photos if full-size version is stored
on the cloud.
Emails.
App cache (most of the "Other" data).


Should be all if not mistaking.