Q:
Dagger/Dagger or Dagger/Pistol for PvE?
I use sword/pistol and shortbow for solo PvE with a 5/6/0/0/3 build. Full zerker with runes of the scholar. Sigil of air in sword, sigil of accuracy in pistol. Shortbow sigils of force and fire.
Playstyle is basically stealth to target, open with pistol #5, then sword #3 (pistol whip) until done. Rinse, repeat. This all you need for any melee encounter.
I would also use S/P in PvE, because of cleave and pistolwhip.
Shortbow in your offhand :-)
Dagger/Dagger is the highest DPS single target weapon sets a thief has, making it one of the best PvE sets.
Dagger/Pistol is one of the weakest options for PvE since Sword/Pistol will do higher DPS while also cleaving and it can drop a blind field just as well.
For a full PvE guide and breakdown of the various weaponsets, check out Chase’s guide on GuildWars2Guru.com.