I think your concerns are valid and may need addressing. You never want to ignore your gut instincts.
Looking at your joint there, I see a bolt which provides a pivot point and only two screws (and glue) keeping it from folding up. This gussetted lap joint is the minimum standard called for in the Zip plans and it prefers more of a gusset where yours is trimmed away to provide a more open hull. This might work in a standard Zip with a deck, but with yours foregoing the cross members and decking, you may indeed have a weak spot in the design.
I would opt for a stronger joint here rather than a minimalist one, knowing that I was going to have a very open utility hull.
Then again, I don't know what kind of stresses your Zip will endure as a tender to a larger vessel.
If it were me, I'd add ply or scrap frame stock to my exposed gusset on both sides until it was level with the frame on both sides. Then, I would double gusset the entire joint in 1/4" ply on both sides. This would raise your strength level to above the strongest recomended design (double gusset), by making it a true 'triple' gusset. It would also be the easiest and quickest fix while compensating for the lack of deck frames.
You'd end up with a very strong laminated joint at 2 1/4" total thickness. That's a lot of material for your chines to get good purchase as well.
That's just my two-bits.
