I think whether it will pass of if the ray will 'spit it out' depends on where the hook is, and if it is 'stuck' into tissue. If it is still in the throat the ray may indeed be able to spit it back up.
We had a Mata mata turtle that was in our collection for over 30 years. Upon necropsy, it had a hook and it was still in fine condition so honestly I think they can persist for a long time. If the body walls it off it will not be exposed to stomach acid anymore, just surrounded by tissue.
It is possible that if the hook is not lodged in the gut that when it starts eating it will pass throught the gut. It will be interesting to see what develops. I'd encourage you to necropsy it if it dies (and I hope it doesn't) to see if your theory about it having a hook is correct. There are lots of other reasons why it might not be eating.