Has anyone else considered using the Deathwatch combat system, i.e. hordes etc for Rogue Trader? I know it will increase battle times, but it might be more interesting and interactive. Any thoughts?

Yes, for certain ship battles ( I had a large fleet engagement between the imperial navy and an ork waaagh going during one session) I think that mass combat rules can enhance the action and help a battle become an adventure in its own right.

During one session, the imperial navy had contracted the players to move a contingent of troops to a warzone as part of the gifting of the warrant of trade. When they arrived they found the imperial navy engaged in a desperate battle with an ork flotilla. The players were in a perfect position to help the fleet considering their transport was equipped with a teleportarium. They proceeded to make several hit an run raids on important ork ships with their imperial guard regiment and helped turn the tide of the battle towards imperial victory.

On the other hand, I think it would be silly to do this too often, as its would make starship combat drag on endlessly.