I've never tried embroidery on hook and loop but I have sewn on a lot of it with regular machines.
My insticts say you want to add it aftewords for two reasons. Firstly it can mess with proper bobbin tension, the hook side espcially. Second if you are doing a fairly dense design than all the theads on the back will effectively mask out the hook or loops making it no longer cling to each other. If you want to try hooping it in I would definetly try the loop side on the theory that it should stitch easier and the hooks can still 'grab' the bobbin thread to a degree.
My insticts say you want to add it aftewords for two reasons. Firstly it can mess with proper bobbin tension, the hook side espcially. Second if you are doing a fairly dense design than all the theads on the back will effectively mask out the hook or loops making it no longer cling to each other. If you want to try hooping it in I would definetly try the loop side on the theory that it should stitch easier and the hooks can still 'grab' the bobbin thread to a degree.