A poly kayak is strongest if you store it on its side. Use some padding where the strap contacts the boat, and it’ll be fine. Wider straps are better (Wider contact point), but not critical. Switching sides every so often is a good idea.
I hang several of my kayaks from trapezes made of rope threaded through hard foam “pool noodles” which creates soft cradles for them. Besides that, the semi rigid noodles keep the loops propped open when empty which makes it easier to slide the boat into them at ground level and adjust the position before hoisting.
I’m a pool noodle junkie – I watch for stores dumping them (around this time of year) for a $1 or less each and always have a batch of various sizes and profiles shoved in the basement loft bin I built for for trim lumber, pipe and conduit.
I’ve used pool noodle for all sorts of projects including with kayaks for flotation fill and for snugging up loose cockpits. I’ve sliced 'em, diced 'em and otherwise abused 'em. Some day, just for the hellovit, I want to try making an entire kayak out of pool noodles, like the lashed reed boats the locals use on Lake Titicaca in Peru.
Storing the kayak on its side should be fine. If the boat has bulkheads, put the straps there where the hull is strongest.
f the question was right side up or upside down, I’d choose upside down. A little deformation of the deck, if it were to happen, will not affect performance. Many people that I know with plastic boats transport and store them upside down on very hot days.