Are there any issues with enabling full encryption and loading custom ROMs or will it be seamless?
Encryption is done on the /data partition (where all app-data is stored). However, /sdcard is sometimes encrypted too (if the sdcard is actually internal memory of the phone i.e. not removable).
If the sdcard is also encrypted,then you will be unable to flash ROM's from within Recovery (recovery can't read encrypted sdcard).
If you have an unencrypted
/sdcard(this is usually true if you have removable SD Card slot), you can install zip from sdcard as always.
If your sdcard is encrypted,too, but you have relatively new device and software(Ice Cream Sandwich or newer), you may be able to use sideload.
install zip from sideloadoption in your Recovery
Run this command on your computer:
adb sideload <filename-of-update.zip>
Then you can continue to flash the ROM. (In my case, the installation process started automatically.)
Encryption it's a software based solution with hardware support. Question is if your custom ROM will support solution. In 2019 I only found one custom ROM which support encryption. It's a AOSP Extended. Other ROMs have encryption options in menu but they didn't work. If you try to enable encryption data partition phone restarts and enter into bootloop. Only formating data partition in TWRP helps getting out of bootloop.