As far as I know
Advantage [Linked]: The ability to dump xorpads or whatever and create cia files.
Disadvantage[Linked]: Every time you unwrap a gift, it will re-wrap itself next time you boot emunand. Also, Whenever you create an internet connection in emunand, it will also make one in sysnand (Not what you want, but easily fixed by deleting the conneciton on sysnand)
Now the advantages and disadvantages of unlinked:
Advantage: No more gift wrapping issue, everything will stay unwrapped now.
Disadvantage: Can't create cia files for DLC or whateever.
Someone can add onto this info.
I'm pretty sure you can still access Data Management fine in emuNAND. The bug is in sysNAND.
I keep them linked so my 3DS isn't nearly useless if for some reason I'm stuck in sysNAND, that way I can still access most of my retail stuff. If the CIA unwrapping issue doesn't bother you, and you remember to stay out of Data Management in sysNAND, then you can go ahead and keep them linked, it's not a big deal.
Thanks for the help guys! I think I'll keep mine linked; I don't plan on installing too many cias anyway so it shouldn't be an issue.