The daggers would benefit from the stealth damage bonus, and their rapid attacks would allow you to quickly chain together multiple magical/poison damage hits, especially if both weapons have different enchantments or poisons on them, while you still get reasonable melee damage, especially in stealth mode from the dagger stealth tree perks without actually having to significantly train your one handed weapon skill.
This was the conclusion I came to. Not only that magic and poison effects could be applied faster due to faster swipes, but the haste rating given to you by the elemental fury dragon shout (or whatever it's called) would speed up your daggers even more, applying the magic/poison effects even faster. Speed is more important than weapon strength when it comes to applying magic damage and especially poisons more quickly.
If anything, the fact that daggers are excluded from the damage bonus would likely indicate they'll be just as deadly as dual-wielding more standard melee weapons, if not more so. The difference will be primarily in that rogues this time around are being encouraged to take up alchemy. They've talked about the poisons that can be made with alchemy quite a bit. Chances are rogues will be able to stack both enchantments and poison on their daggers, making them outright killing machines.
I hope they use the kind of poison that doesn't spoil the succulent Mud Crab flesh, though.