Duck shoes might help as a temporary solution, very short term, but finding something to go over the cement will, I think, be easier and healthier.
I have duck shoes and they can be tricky to get on correctly and keep on without restricting the ducks' circulation.
I use towels for bedding, it should be fine to use them. If your floors are a smooth surface, that should be fine. It's the coarse, unfinished cement that really abrades the bottoms of their feet.
So having stall mats or similar on top, that can also be easily cleaned off can help. Or a nice sawdust or wood shavings or straw base might work well for you. Some folks use sand.