When I do a iPhone restore using iTunes why all apps settings is lost?

An encrypted iTunes backup will save most but not all passwords, some institutions (like some banks) will force you to sign back in with your password, regardless of encrypted backup. It is up to the app developer to manage this.

But Wi-Fi, Bluetooth, Health data, etc. all seems to be restored through an encrypted backup.

Which type of iTunes BackUp did you Restore from, there is normal or encrypted, the latter backs up far more sensitive information and therefore can restore far more back to the device.

About encrypted backups in iTunes - Apple Support

If you are saying certain apps require there logins to be entered following an Encrypted Restore then may be it’s an extra layer of security.

The only way to get around this that I’m aware of is to put your device into Recovery Mode when connecting to iTunes, you then get the option to Restore or Update, the latter will try and just replace the iOS which touching your data/apps, which should mean you will not have to re-enter app passwords.

rockmyplimsoul wrote:

An encrypted iTunes backup will save most but not all passwords, some institutions (like some banks) will force you to sign back in with your password, regardless of encrypted backup. It is up to the app developer to manage this.

But Wi-Fi, Bluetooth, Health data, etc. all seems to be restored through an encrypted backup.

Yes, good point, but the Banking App I use lets you set up a "passcode" so even though you are "forced" to login each time you use it, it's not a big issue (you can even enable Face ID once you have done the initial login so thereafter is even better).

Not sure what else to add, whenever I’ve restored from an iTunes encrypted backup I can’t remember having to re-enter app passwords, certainly never for my mail accounts, so not sure what’s going on.

May be someone else will come along and add more, but as far as I can tell the “iTunes encrypted backup” is the method that backs up the most complete data from your device.