Having a dagger-using Rogue suffer from damage reduction twice in exchange for being able to handle enemies without armor isn't exactly selling me on the idea.
I believe that you're trying to say that such a double-dipping penalty would be compensated for with increased damage onto targets which don't have armor beyond what standard weapons give.
I have concerns about balancing Rogues for being strong against unarmored targets and very bad versus armored targets. Unarmored targets by definition are likely to be easy to kill for all physical attackers, and since they're likely to be spellcasters or archers, they're also likely to be priority targets for everyone anyway. And if the only enemies remaining are armored (which will likely include more than a few bosses), that'll make the Rogue much less useful in combat.
Personally, I would balance this by making it very easy for warriors to be physically blocked, whereas rogues have the potential to more easily slip past the zone of control of heavy warriors and slip through to mages.
But you're right that I've only considered this from the perspective of group vs group balancing. If D:OS is going to continue to have Group vs Boss battles, then there should be a way to coordinate this so that all team members have the opportunity to contribute.
Anyway, I'm not suggesting that all of this is the best way to design rogues, but it's one way that the "double attack" is more than just cosmetic. Another way is that with your chance to hit being rolled twice, you're more likely to hit at least one of the two hits. And of course, you're carrying two weapons with different enchantments, so there are other potential differences as well.
I'm not saying the differences will be good or significant or interesting, but I'm sure there'll be at least a couple of differences which have a real effect on the gameplay.