I've always had this problem too, so we actually sectioned off two of our paddocks into four smaller holding areas. That way we could rotate when one was getting too slippery from hooves churning up the mud.
As long as the horses have somewhere they can stand that ISN'T flooded, like the higher part of the hill, then in theory it should be fine. Just keep a close eye on their hooves, lower legs, etc. in case they start getting any issues from the wet.
Satin Reign aka "Misty"... my life, my love, my everything.