If you store the kayak hull-down on the foam, the foam compresses less.
But if the kayak is stored on its side (as if on crossbars with a riser), there is more weight concentrated on a small area. This causes more compression underneath.
I've kept sea kayaks stored each way and have noticed that method #2 definitely results in more compression. Don't use pipe foams, because they're toast after a very short time.
If you angle the kayak at close to 45 degrees, that may help reduce the load on the foam underneath.
1 Canoe/Kayak Trailer
Pull-Up Strap Handle Kit
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