It gives you two separate folders for managing data. Basically, this means your sysnand and emunand can act independently of one another as they install and read data from two separate folders (On your SD card). The benefit is that you don't end up with strange occurrences (Like games rewrapping on boot, etc) because you're not sharing a data folder between two nands.
Unless you have some pressing reason why you can't unlink them, you should just unlink them.