Interpreting the data is completely unimportant, as it will be another GBA that will be recieving it. In fact, the only real problem is in keeping the data intact as it goes across the internet, and then sending it to the other gameboy in the same form that was sent over the internet.
Lag MAY pose a problem, since distance will be taken into account. When you hook up your gameboys locally, the data only has to travel a few feet. On the internet, it will have to travel much longer of a distance. Whether or not this will be a problem isn't for sure, though, and I hope it won't be.