Use latest vcpkg commit in configuration, sync manifest with deps.txt (#23554)
### Description
`python3` dependency is removed in `onnx` port of
https://github.com/microsoft/vcpkg upstream.
* https://github.com/microsoft/vcpkg/pull/43236
*
https://github.com/microsoft/onnxruntime/pull/23285#issuecomment-2579073056
(Previous work)
Removed `nsync`, and use ONNX 1.70.0+ in vcpkg.json(manifest)
### Motivation and Context
* Help #23158
* #23456