Semantically correct IMHO would be to keep an empty cell really empty. However, I, too, fill empty cells with s for pragmatic reasons.
As for screen readers, I’ll have to make an educated guess: Empty nodes will likely not be read, because HTML consists mostly of whitespace text nodes, which readers ignore, and I assume, that is collapsed to a simple space in reader applications (since non-breaking is a property of visual media).
For rendering visually, one could rely on the CSS table property empty-cells:
table {
empty-cells: show;
}