Re: speaking as a bee/zee shipper too (not an otp, but still'd be cute)
Sure, he's paranoid, but he's paranoid about everything and everyone - I think he could probably get over this particular bit of paranoia, given the long history that him and Zatanna have. The way I think he'd get around it? A 'no magic in the house' rule, similar to his rule that no one wears costumes while upstairs in Wayne Manor.
'All right, you can do magic down in the cave - BASIC magic, the put-your-costume-on type, no summoning of demons or anything - and magic is fine when we're out on a case together, but NO MAGIC IN OUR PERSONAL LIVES. No cantrips in the closets, no bewitchments in the bathroom, no levitations in the library - no magic! That stuff makes me antsy. Keep it downstairs, please.'