The only imbalance was for fort sieges, which are for a tiny part of the day, and that was caused by more people rolling Elyos than Asmo.
Nowadays the factions are way more balanced since Free to Play kicked in, and people can just open another account if they want to swap factions.
Back then, if you rolled an Elyos toon on Nezekan you were stuck with playing Elyos unless you wanted to fork out for a second monthly subscription just so you could roll an Asmo as well.