This stuttering is most likely related to the error (or rather hundreds of them at a second), caused by the breathless at some point. Turning off object shadows might increase your performance in general, but in case of intermittent stuttering as you said, it has to be a memory leak (check the console to make sure). To get rid of this, simply save and load the game (use f5 and f9 hotkeys if you want) or just stop the ship. This issue will be fixed in the upcoming update.
Also, thanks for playing and supporting the game <3