Frankly, I've never considered what Martha does with the scraps, but I've wondered about where she gets all her fabric. As often as Superman's suits get damaged, she needs a pretty steady supply, even if she's just replacing the capes. She can't be just going to the local fabric store in Smallville; that would raise too many questions. She needs a steady supply of the same type and color of fabric. She could send Clark to a new fabric store and have him buy out their whole supply each time she needs more, but he's not likely to get the same fabric each time. I was thinking that maybe they contracted with a fabric manufacturer under an assumed name or a shell company or something.
As far as the scraps go, maybe she shreds them and uses it as filler for pillows and puffy blankets.