It's potentially still more than just cosmetic. For example, say that armour has a damage reduction effect. For two attacks, you get affected by the damage reduction twice. However, this is balanced by providing the daggers with very high damage potential on unarmored enemies.
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.
Crossbows shoot in a straight line, while bows have an arced path of flight.
Oh right, I forgot that. Yeah, that's good enough differentiation then, with the apparently increased use of height in the game.
Another great way to balance Daggers... is to...
Not even try so to speak. Make it so Rogue skills rely on the Dagger.
Alternatively:
for the dagger is it could be pitiful in taking down Armor HP, yet great in taking down Raw HP and especially enemies who are compromised.
Daggers are all about opportunity.
Or you could give Daggers the ability to ignore Armor HP or ignore it in certain conditions. (truthfully that can be... a disadvantage, as enemies with Armor HP won't take CCs)
Honestly I can picture Rogues in this game basically being the kings of taking enemies once their Armor is gone. With Warriors being the armor killers.
As I said, I'm hesitant of trying to add rock-paper-scissors countering to physical attacks, in a game which is about letting you have so many options.
Final Fantasy X has such a system for physical attacks. The party (7-8 people, maximum of 3 in battle at once) has Tidus as a hard counter to fast enemies, Auron as a hard counter to armored enemies, Wakka as a hard counter to flying enemies. The key thing though, the reason why the RPS system for physical attacks works in FFX is because it also allows you to swap members mid-battle.
In D:OS 2, the party has 4 characters at a time and can't switch them mid-combat. I don't think it would work well for the role of Rogues to be "okay they're garbage at the start of the fight, but once the Real Warriors do their awesome stuff, the Rogues can finish off the rest, even though the Real Warriors are actually equally effective at all stages of the fight".
That's why my suggestion was not about trying to figure out balance by making Rogues out-damage warriors in some circumstances and under-damage warriors in others. Instead, giving dagger-users a much higher chance to dodge physical attacks, lets them get into combat and use their FIN to sustain their lives in combat instead of their CON. Tying that extra dodge chance to the dagger instead of FIN also means it only affects Rogues and not bow-users, who would also have high FIN, but they use distance to stay safe.
EDIT: The same bonus could also apply to some other (specific) FIN-based melee weapons if you wanted to give the Rogue more weapon variety than just daggers.