I've noticed the same issue with my toes in my Nike Free Crosstrainers. I'm thinking flexibility is some of the issue because I ride my mtb with low top hiking shoes and have never had an issue. They're way too clunky/heavy for my road bike. I have Zerfas mini clips (just wrap over the toes of my shoes) so anything chunkier than tennis shoes don't fit too great.

A friend that has rode the Seattle to Portland (2 day double century) 4 times wears basic Pearl Izumi mtb shoes without any cleats (left the rubber cover on). He really likes them a lot since they're sturdier than standard shoes and more breathable. He also uses Power Grip straps so there's lots of ways to position the feet. So maybe making a conscious effort to vary the foot position a little can help keep the blood flowing.

Another possible variable is the laces. I have serious problems with my feet falling asleep on my snowboard. It's typically when I get the strap over the top of my foot too tight. The main vein to the foot runs along the top so if your laces/straps/binding are too tight as the feet swell its easy for circulation to be constricted.