NYT reported Zooey Deschanel was named after the J.D. Salinger book Franny and Zooey. This Salinger-Deschanel pathway appears to be the most reasonable explanation as to how this spelling has become fairly common.
Even if it's "Zo-ey", I will forever pronounce it "zoo-ee" in my head. If the name is said like "zo-ey", spell it like "Zoey" (zoe works too). Zooey is just weird. What on earth are people thinking? It's like saying Chlooey is pronounced Chloe or Ramoona is pronounced Ramona: it doesn't make sense.
https://en.wikipedia.org/wiki/Zooey_Zephyr