1- I don't know if there is a limit to such a stay (being in H1-B status and then staying out of USA) but AFAIK, staying out of USA for genuine reasons is totally OK and you will not lose your status. Yours is pretty sound.
Remember, INS/BCIS allows you to work (grants permission and issues H1-B Form I-797) in a particular status (i.e. H1-B in your case) for an employer in US, it does not dictate rules of employment, that's an arrangement between you and your employer. INS rather sets the rules for you to stay in that status and the steps you have to follow to keep your status valid. If your employer has granted you the leave to stay out of US for some reason, then you are good to go. INS does not care.
Here are 2 FAQs from INS/BCIS website which will help you in understanding this better.
http://www.immigration.gov/graphics/howdoi/h1b.htm
a) Must an H-1B alien be working at all times?
As long as the employer/employee relationship exists, an H-1B alien is still in status. An H-1B alien may work in full or part-time employment and remain in status. An H-1B alien may also be on vacation, sick/maternity/paternity leave, on strike, or otherwise inactive without affecting his or her status.
b) Can an H-1B alien travel outside the U.S.?
Yes. An H-1B visa allows an alien holding that status to reenter the U.S. during the validity period of the visa and approved petition.
2- How could there be any taxes (City/State/Federal) on a pay which will NOT be paid to you! As you mentioned that you will be on unpaid leave, thus you will NOT be paid your usual salary, which means no taxes either.
Also just to clarify, income taxes are paid by YOU on your salary, not by your employer. Employer just uses a system to automatically deduct them from your pay and forward them to related (federal/state/city) authorities.
Hope this helps!
Regards, -Amir
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