We never had a problem with pellets falling thru the dog excluder layer, just with the cage bottom itself.
In the future I am thinking of a hutch-within-a-hutch design that features a solid sided bottomless shed with dog excluder and then a hanging cage inside that can be pulled out for cleaning or replacement. We have cats, dogs, raccoons and (eep!) rats here in town, so sturdy is important, but I just don't like wood for sanitation (and in rainy Washington, for rot).
I was thinking for making the "solid sides" out of corrugated tin or fiberglass so that they could just be pressure washed. Pressure treated 4x4s for legs, 2x4 for the framing and the rest tin and wire. I'll let you know how it goes. I am building this in about a week or two, I hope, new buns coming!!