If Greninja changes type after being poisoned, it will continue to take damage from being poisoned. It won't absorb the Toxic Spikes either, because they're absorbed upon switch in, and Greninja was Water/ Dark upon switch in.
It's the same with Gengar/ Crobat being unable to absorb Toxic Spikes, even if something like Smack Down or Gravity is used on it when it's on the field.
We also know that Greninja will continue taking poison damage because it's the same mechanics as Soak. If a steel/ poison type Pokemon has Soak used on it, it will become susceptible to poisoning. After being poisoned, it will switch out and revert to its original typing. However, when in battle again, it will continue to take damage from poisoning, regardless of it being a steel type again.