So there is an option to set the default subtitle language in Plex, but I don’t think there is an option for default format. You could use MKVNixTool to go through and change the default or remove the tracks in the MKV’s themselves, or vote on some of the feature suggestions asking for more control over subtitles.
Control subtitles on a per-series basis - Feature Suggestions - Plex Forum
Default tracks language setting per library - Feature Suggestions - Plex Forum
