Comments apply to the 23-Nov-11 review copy that I have...
As an SFU player, I very much prefer the new ablative "shields" (actually armour in game terms) the ships have. Works more like the base games. The opponent knocks down a shield and damages your ship a bit, but then you maneuver and turn a fresh shield... So it feels very like how it works in SFB/FC, even if far more abstract.
And it's not faceted any more either, which was a fiddly bit when controlling large numbers of ships. Yes, there is a chance that an unlucky die roll will knock out your ship's main armament. However, if you're running a reasonable number of ships (3 or more), it's not going to be a real problem, because an unlucky damage roll on a single ship will have less effect.*
The copies of the Fed CA and Klingon D7 ship sheets that I have (the revised kind with the illustrations on them) lack weapons damage check boxes.
I don't know if you're rolling less dice. You're rolling a bucket of dice once per attack, rather than one-third of a bucket three times. It's still faster.
*I prefer the simple method of just apply degradation to all ship's weapons myself.