I'm not a native English speaker, and I though asking "Where could he/she had gone?" was very common. But when I searched that phrase in Google I got only 6 results.
Is there a more simpler, more common way of asking that question?
You got only 7 hits because you have the ungrammatical “could had gone” instead of the correct “could have gone”. If you fix your had into a have, it will be fine.
There are 11,900,000 links for this where could he have gone. Is that the question you want to ask?
I usually would say "Where'd [s]he go?"
The "could had gone" may indicate worrying if [s]he will ever return. If you want to convey your concern, then you should stick with "Where could [s]he had gone?"
Edit: I missed that "had gone" should have been "have gone". Thank you.