As Mick said, he wont go into reasons... and the only reasons I can think of is the AN gives info about what you are looking at... maybe its better than what the sky/synscan controller on the EQ6 does (if it gives any)
Mick - what do you mean by hooked up? The AN can be attached to an EQ6 pro goto as it uses its own encoders. You can connect either the EQ6 hand controller or the AN to a PC via a serial port. I haven't tried to connect both but I assume it is possible if you have two serial ports with different COMM numbers.
If you are looking for an AN and EQ6 hardware kit - I've got one going cheap!