I never tried with Hebrew or any other language... although I have used foreign symbols in some of the documentation I had to do. The thing is that that I always use Word (or similar) to write the text, but then I import it to InDesign (or similar) to do the final touches and fits on the pages... These softwares are able to convert to ePub or Mobi, among other formats, and I never had a problem.
Obviously, InDesign is expensive but I'm sure that there's a similar software that can do the same job. I can't suggest any beause, for this kind of jobs, I always used InDesign, Illustrator (if it is a flyer or similar) or QuarkXpress