I don't understand the question, if they are hard coded then the subtitles are part of the image frames themselves and as such will be retained when converted to .mp4 or .vob
.mkv's usually have soft subtitles, in which case you'd check if you're destination container supports this and convert accordingly. If it doesn't support soft subtitles then you need to re-encode the file with the soft subtitles to essentially make them hard coded. You want to avoid re-encoding video to retain quality so stick to soft subs where ever possible.