I am not sure if you understand if Carl Zeiss and Zeiss Jena are entirely different companies. Perhaps you understand this and this is what you are getting at when asking about what is the correct hood. It seems to me that Carl Zeiss versions of this lens and Zeiss Jena versions are certainly different in some details - possibly including filter ring diameter and hood type.
But one thing you posted put a thought into my mind that there is a possibility that something else is amiss - you said that your lens is a Carl Zeiss Jena and is
prewar.. However it is my understanding that lenses marked Zeiss Jena were only made after the war, not before and was done by Russians and East Germans to avoid copyright issues upon being sued by the real Carl Zeiss company in West Germany for holding out their lenses as being Zeiss lenses. (At the end of WW2 Russia confiscated lens designs and machinery of Zeiss and began using these to replicate Zeiss lenses badged either with Russian names for the camera - Kiev or as East German Zeiss Jena lenses). Hence you can see the potential issue if your lens was sold as prewar but has a post war marking. It suggests something may be amiss in that respect and if that is so it may also be why your hood does not fit (possibly). or maybe you are just acknowledging that the Zeiss Jena lens is built to a prewar design - which is certainly true.
As you have not posted an image I cannot tell if there is something that would worry me about your lens. The following articles give some info on how to discern a fake from a real Zeiss lens and a Carl Zeiss lens from a Zeiss Jena one. Good luck.
http://www.klassik-cameras.de/Zeiss_Fakes.html
http://www.zeisscamera.com/articles_JenaContax.shtml
http://leicaphilia.com/carl-zeiss-jena-sonnar-5cm-1-5-for-leica/