Nymeia is the goddess of luck after all though, and a coin is very symbolic of that, so it makes sense to have her visage on the 'heads' side (also, she was not worshipped by any of the citystates, save for that brief time in Ala Mhigo, so it might have been decided to choose her as a neutral figure rather than 'playing favourites' with another deity who happened to be a guardian of one of the cities, like Nald'thal).

Also, I suspect gil is far older than even the Allag, seeing that npcs back in Elpis give it in quest rewards and that gil is accepted by the stores there (altough that could just be for gameplay purposes, like in ShB how G'raha said the stores in Norvrandt would accept gil even though it's not their native currency due to the relative value), and, given that the Allag was founded by Emet originally....

That's just my own musings though.