If i disable all 3D Funtions within Kodi the Subtitles are displayed like they should but this sucks very hard because of 2 issues.
That doesn't sound right. Have you produced subtitles with two copies of each subtitle (e.g. duplicated SBS or TAB).
You don't want to do that. When playing a 3D video kodi will automatically duplicate the subtitles in the correct manner
(may be Frame packed, SBS or TAB).