Hard to say. I live on a creek that serves as an inlet to the lake. They drop the water level about ten feet in the winter for fish spawning or something. I see some people leaving their pontoon boats and houseboats just laying in the mud after the water has receded. Don't know how good that is for the boats, but they do it every year.
As long as the motors out of the water and the toons are not sitting on rocks, should be OK. If mud bottom, shouldn't hurt it. I've seen this too at several lakes. Plus, they set pontoons on foam blocks for months with no problems. Should be fine! I would think that if the water froze and it's only a couple of inches deep, it would just lift the boat a bit.