I went through a similar weapon choice issue with my nightblade. Started out with a two-hander, then tried dual wield, went back to the two-hander, then tried shield, then back to dual wield, then back to the two hander again, and now i'm using a 1h/shield again lol.

All that experience says pretty much this:
-Two handed if you want to kill things quickly. In burst damage, 2h is king. Uppercut from stealth is insane.
-Dual wield works best with siphoning strikes for returns, and has higher sustained damage than the other two, but seems to lack in burst and utility.
-1h/shield is highest on utility and survivability, but lacks in damage. However, nightblade class skills can really help make up for this.

Overall the differences in sustained damage are very small, all three weapon setups are capable of functioning in the damage role. Shield will let you survive better and give you better debuffs/utility abilities. Dual wield will give you an edge in sustained dps and resource recovery. Two handed will give you better crowd control and burst damage.

Mind you all my experience is using this with medium armor.