Ok so everything is working fine with ssh after each restart etc. I was also experimenting doing it by the phone terminal but when I go that route I only get half of my config working. For example, the contacts are not visible, the changes made with UTweaktool are not present, the keyboard theme etc. Sadly for some reason doing it by the terminal only decrypt half of my config or something like that. I don't know why.
Also I noticed a worse battery perfomance in my Nexus 5. It was 65% 8 hours ago before going to sleep and today in the morning the phone was dead. Other than that. I will try to figure out why decrypting the phone via the terminal is not working for me, if I manage to get that working or by a script/bash alias I will keep with the encryption long term. Let's see.. Thank you again.
One more thing, I am also experiencing the wifi dissapearing sometimes, usually I fix that by restarting once the phone.
edit2: after trying to decrypt with the new commands, it worked well doing it from the phone terminal