[wasm] upgrade emsdk to 3.1.44 (#17069)
### Description
This change upgrade emsdk to 3.1.44.
Because backend is upgraded to LLVM 16, so need to fix a lot of build
failures caused by "-Wshorten-64-to-32".
most of the build failures comes from generated `onnx.pb.h`, and this
can be fixed by including "core/graph/onnx_protobuf.h", which detects
and ignore shorten-64-to-32 warnings.
