No. Ninja is an alternate class of Rogue. Just like with archetypes, it isn't actually a separate class, and can't be used to multiclass with itself. You can't be a Rogue 1 / Ninja 19 any more than you could be a Rogue (Rake) 1 / Rogue (Poisoner) 19.
It's probably the dagger archetype that grants d8s when using daggers but d4 for any other weapon.
Where is the 1d8 sneak attack coming from?
If it's a Rogue Talent, then Ninjas can take those.
Two sources:
Knife Master:
A knife master focuses her ability to deal sneak attack damage with daggers and similar weapons to such a degree that she can deal more sneak attack damage with those weapons at the expense of sneak attacks with other weapons. When she makes a sneak attack with a dagger, kerambit, kukri, punching daggers, starknife, or swordbreaker dagger, she uses d8s to roll sneak attack damage instead of d6s. For sneak attacks with all other weapons, she uses d4s instead of d6s.
This ability is identical in all other ways to sneak attack, and supplements that ability.
Skulking Slayer:
At 3rd level, when a skulking slayer charges and makes a sneak attack with a two-handed weapon, she rolls d8s instead of d6s for her sneak attack damage.
This ability replaces trap sense +1 and +4.
Ninjas could get it, but I'm horribly confused on archetypes on alternate classes. I'm pretty sure he's talking about the Knife Master in this case.
(Me, I'm playing a Skulking Slayer/Scout in PFS.)