Hi Trevor,
now i get the chance to help you out for once, not always the other way ;-)
we sikaflexed the complete tipup canopy without a single hole in the canopy material...
yes forgo these holes.
have you built the rollover bar yet?
we built both the canopy frame (width) and the rollbar (width and height) a tiny bit undersize, so that there is a small gap between plexi and frame in the end (which is being filled by the sikaflex)
sikaflex requires a minimum thickness of its layer to form a strong bond (check the spec sheets). if the frames are built per plans and the plexi is not spaced, the sikaflex can not use the generous available area of overlap for the primary bond. chances are it would still hold great via the fillets in the corners, however, if you can account for it from the beginning, why not do it.
rgds, bernie