Out of boredom and some other reasons I actually tested this a few weeks back. The damage from the Dual Wield hit seems to most definitely be calculated based on the offhand weapon, despite some people saying otherwise. I only did a few tests, but I'm satisfied.
Test #1
Job: 55RDM/27NIN
Targets: West Ronfaure Wild Rabbits
cRatio: Capped @ 2.00
Main: Bronze Dagger (DMG:3 + fSTR:8 = Base:11)
Sub: Bronze Dagger (DMG:3 + fSTR:8 = Base:11)
Weapon Skill: Wasp Sting (no WSC modifiers or fTP bonus)
Projected Damage: 34 - 56
Actual Damage: 38, 43 (a whopping two tests)
Test #2
Main: Bronze Dagger (DMG:3 + fSTR:8 = Base:11)
Sub: Auriga Xiphos (DMG:17 + fSTR:9 = Base:26)
Projected Damage: 58 - 94 (assuming each hit is calculated per weapon)
Actual Damage: 81, 86 (again another whopping two tests)
Both times with the subbed Xiphos I doubled my damage. More tests would be necessary to have a sample size of more than 2 tests each, lol, but I have faith in the math of capped pDIF (with or without the 1.05 randomizer), and each test fell nicely into the projected values, so I'm satisfied unless proven otherwise.
As most people know, the Damage Type modifier (Blunt, Piercing, Slashing) is the same for all hits, and based on the standard damage type of the Mainhand Weapon (no exceptions for stuff like Degens or anything). I tested out how Jump works too, and in that case Damage Type IS calculated for each swing (as well as calculating the damage separately as illustrated with the WS hits), and exceptions like Degen will switch the type for that hand.
Based on all these separate calculations taking place as far as damage goes, I'd also assume that Accuracy and Attack are calculated separately for the offhand weapon as well, but I'm not about to actually test it. =p If you're getting the full damage from an offhand weapon, I really doubt SE's going to let you have that for free is your Skill with that weapon is 0.