Not at all. This has nothing to do with Linux. Whenever you plug your phone with a data cable to a computer Android gives you a couple of of choices with which protocol to connect. E.g., you can only mount the SDCard, or, via the MTP protocol, also your phone’s internal drive. Just when you want to use ADB you need to uncheck all possibilities, which Android calls installation mode.
So whenever you connect a phone with a computer, you should get that kind of choice by swiping down from the top. If you don’t, maybe you are not using a data cable (4 pin cable).
If you don’t encrypt it manually (e.g. with some 3rd party app; Android doesn’t do it by default, unfortunately), it will stay unencrypted.
You don’t need to flash openGAPPS for every update: A) openGAPPS updates may only be updates in the code of how to install GAPPS; B) GAPPS, or I call it here GMS (Google mobile services) will get updated automatically when theu are installed (and you have a Google account account) in the background; pulling the updates right from Google.
So once you have openGAPPS installed, you will only need to reinstall it, when you update your FPOOS version.