I think the original question deserves a Cuban to answer it. And as a Cuban I feel it totally appropriate to answer the Habana, Havana question.
So ... the real difference is that if you are a Cuban in Cuba you would call Havana, "Ciudad de La Habana" because that is the CORRECT format, spelling and pronunciation in Cuba. As a matter of fact we Cubans don't even enunciate the H at all. A real Cuban saying Habana would sound like La ahbana.
Whether your cigars say Havana or Habana have everything to do with whether or not they are actually Rolled & MADE in Cuba. If they are Cuban Seed ONLY you will more than likely see the word Havana, In Jamaica, Bahamas and most other nearby caribbean neighboring countries, if you purchase a Cuban, they will say HABANA, Cuba because they are most likely 100% real grown & rolled in Cuba. Although BEWARE there are many fakes anywhere you go. Depending on the brand you buy there are identifying factors on real vs fake. Just my 2 cents worth and experience.
And if you want to legally experience a REAL Home Grown & Rolled Cuban, go to a neighboring island. Look for the ones with HABANA bands/stamps verify authenticity and enjoy!
Anything else is just Cuban seed grown who knows where and claiming to be a Cuban which is in no offense like a Puerto Rican, Dominican or Mexican claiming to be Cuban. There is a BIG difference. Our Coffee, Our Rum, Our Cigars Our Sugar Cane and of course Our Women are ONE and ONLY
P.S My maternal grandmother was born in Cuba in 1899 while Cuba was under US occupation and her trade as an adult was primarily as a Piano professor and her evening job as a single widowed mother of 9 children was rolling and banding PARTAGAS cigars in the Partagas Factory in Habana, Cuba
which to this day is still a MAJOR tourist attraction in Cuba. So I do have a little 1st hand knowledge passed down from my grandmother who lived to be almost 103.
Cheers!
References
http://www.cigaraficionado.com/webfe.../show/id/16124
http://www.cigaraficionado.com/webfe.../show/id/16209