Before I went and bought a carrier to hold two kayaks on their side this winter, I had planned to build my own version. I still think it's a decent idea so I'll present it here in case someone wishes to implement it.

Here is a Google Sketchup drawing of the kayak cradle I envision. It would be constructed of plywood lamination with fibreglass or maybe carbon fibre for additional strength, and a pair would be used though only one is shown here. Bolts on the underside would clamp it to the load bars. The U-shaped portion would be padded, and straps would go from the outer holes to the top hole to secure the kayak on the cradles.

Cheers,
Bryan