When I run wasm-opt -O3 myfile.wasm, I get no error and no output, but myfile.wasm stays the same. This lead me to believe that these files had already been properly optimized.
Then @kripken told me that I had to specify an output file like this: wasm-opt -O3 -o myfile2.wasm myfile.wasm.
I think my first command should error.