Use onnx_protobuf.h to suppress some GCC warnings (#23453)
### Description
Use onnx_protobuf.h to suppress some GCC warnings.
All the changes are autogenerated by a shell command.
```bash
find . -type f -exec sed -i 's/#include\s\+<onnx\/onnx_pb.h>/#include "core\/graph\/onnx_protobuf.h"/g' {} \;
```
### Motivation and Context
This PR is needed for making vcpkg work(without disabling all warnings)
This PR is split from another bigger PR per request from a reviewer.
