The problem is, without removing the hatch from the deck first, how do I know where to stick down the sacrifical weather stripping being used as a pattern?
My only thought so far is to make a paper pattern from the layout of the hatch on the top of the deck. Drill a couple small locating holes through the paper and the deck then match the paper to the holes on the bottom side of the deck. Sounds a little crude to me but the best I got so far . . . . that leaves me holes to patch no matter how small I drill them . . .

Randy-
I don't think you need to drill any unwanted holes, but I may be missing something.
I'd just use the center line of the boat - where the strips meet - as one orientation line.
You can measure the fore and aft location from the cockpit recess.
You can mark the underside of the deck with a felt-tip (Sharpie) marker - the markings will be protected by your Contac TM 'mold release' film. If you repeat (trace) the markings on the Contac film side that you'll be glassing, the ink will transfer to the glass layup. (Assuming you aren't using black resin, you'll be able to see those marks later.)

When it comes time to cut out the 'hatch cover', you'll need a row of small holes to start the jigsaw blade - you can drill those from the underside of the deck.

If you do feel you need to drill locating holes, a 1/32 (or smaller number drill) hole in the mid-deck strip joint won't be very noticeable (to anybody but you). You just need a hole big enough to push through a stiff wire - a guitar string cutoff will do nicely.