Efficiency
Ductwork is intended to be more space efficient than Hoppers in many situations (but the most efficient systems generally involve a mix of Ductwork blocks and Hoppers). It is also intended to make it easy to design item movement networks that require less system resources (particularly from the server). This is in part because the Duct block does not have any item extraction code and also does not have any code for disabling the block with a redstone signal. Both of these Hopper features are moved into other blocks (the Collector and the Damper, repectively). Ductwork networks are typically mostly comprised of the Duct block.
Ductwork blocks always try transfer API methods first (where available) before using Minecraft inventory methods. Given the transfer API is an abstraction layer when handling Inventories, and also its use of transactions, this is likely a little less efficient. In my opinion, the small sacrifice of efficiency is worth the probable increase in cross-mod compatibility as more transfer mods start to use and implement the API.
(This was only true until version 0.3.0. My kid really is perfect now...)
You will probably still also use Hoppers! Not everything is just automatically better with Ductwork:
