Yes, I looked on that link and E is for the Northern countries and L for the Southern ones. It might have something to do with the way the majority of air routes flow, ie. N-S or E-W, I've been told.
Nice idea with that Latin thing but I don't think the people who thought of these codes really care about something like that. Never know though! haha
When I looked at the country codes, I realised, they should definitely make the airplane call sign codes the same as the country codes. Would make life so much easier!