If you have problems with new "Steam Deck compatible" version, more specifically some audio is still missing for you, most likely you were using xaudio2_9 dll trick as I did. Took me a few redownloads but I managed to figure out what to do. In short, remove any custom launch options and deselect custom proton version. Uninstall the game and delete any residual files and folders for MGS2 in steamapps/common. After you redownload the game sound should work.