NEO-O were the earliest models, then for reasons I can't say they changed it to NEO-AEC.
I noticed something though, I bought a boxed joystick from a store here a few days ago and it came up on the receipt as NEO-O.
Anyway, these days there is a price difference as the NEO-O system for example, in the white box, will go for more money, just like the joystick when in an original run box. Functionally... well the earliest systems had yet another different motherboard although since I can't say when the black boxes began to be used, you might find that same board in some of the black-boxed systems as well.
In conclusion: Unless you want to collect, it makes no difference at all.