If I encrypt my phone will I still be able to load custom ROMs? 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).