I've also been struggling with numb toes, starts with my 2nd smallest toe on each foot and moves inward. I have wide feet and still riding on flats because it's so hard to find wide SPD shoes at reasonable prices. My main cycling shoes are at least 1/2 or 1 full size too long to accommodate my wide foot and I've mostly associated my numb toes to saddle fit/sciatic nerve as mentioned above. If I'm riding in the city and getting out of the saddle to stand at red lights my feet/toes hold up better than long distances on trails without relief. I've now tried several saddles and I'm not so sure it's the saddle fit, so I'm back to shoes.
Looking forward to warmer weather so I can ride some distance in open toed sandals and see if I still get numb feet... that ought to at least eliminate one question.