I'm just wondering if any of the new Unchained rules for Rogue apply to its Alternate version the Ninja. I've read sometimes that the Ninja is essentially a more complex archetype for Rogue...so...
This is pretty firmly in "talk to your GM" territory. By PFS rules it's a no, but it would be an extremely straightforward conversion so there's no real reason not to.
Yes; the biggest sticking point by the rules is that the rogue talent list received a lot of modification to go with the new rogue whereas the ninja trick list is unchanged.