You can try it. They might scratch all the hay out, or they might be fine with them. They also ight lay in the corner of the stall, or wherever they want, though!
Is there a roost in there that is higher than the nests? It would be a good idea, as they will usually sleep on the highest point, and you don't want them sleeping in the nest boxes or you will wind up with poopy eggs. Be sure the roost has some width, like the wide side of a 2x4 or a fat branch, for the comfort of their feet.