It can get even more complicated. A Shortsword is indeed a +3 weapon, as is the Dagger - so the choice is +1 to hit versus +1 to dmg. However, you can also pick up proficiency with a Rapier with a feat, which is a light blade that does a d8 instead of a d6.
Hence, I would imagine a rogue would probably start off using daggers (for enemies who're harder to hit than normal), shortswords (for the extra damage on easier targets), and shuriken (because with the rogue weapon talent, a shuriken most likely is a d6 instead of a d4). Once you level up to get your hands on a Rapier, you'd probably still keep the shortsword for off-hand or as a spare, while the Dagger remains useful for those situations where you need every possible + to hit. Lots of weapons for the Rogue. (Did I also mention that the Scimitar is a light blade with high critical?)