There's no clear rule adding any detail on how to handle it in any particular way.
I assume it works as usual:
If it's a deliberate attack, roll to hit either the rider or the mount, whichever was aimed for.
If it's an arrow passing through that wasn't aimed intentionally for either, you'd use the rules for hitting the wrong target etc. I'd probably roll once to see if either is hit, and if so, roll randomly to see which one is hit, as with shooting into a HTH hex.
(However I think there are issues with rolling to miss in TFT, and prefer to use
my TFT house version of the GURPS method.)