No, baking soda is not safe for rabbits! Baking soda can lead to serious illness (e.g. respiratory problems and gastric problems -- see the related link below).
Also, baking soda just isn't a good way to reduce bad rabbit smells:
(1) It might mask the smell a bit, but it won't remove the ammonia -- and ammonia is toxic: it can lead to respiratory problems.
(2) It won't work as well as white vinegar. Scoop the litter box every day or two, and clean it with vinegar once every month or two. Vinegar works best for cleaning up dried urine, and it also kills bacteria and eliminates the smell of rabbit urine and hormones. If there's a lot of dried urine build-up, soak the litter box in vinegar for a few hours and then wash it in hot water.
Spaying/neutering also usually leads to limiting smells in your rabbit, and some litter materials (like aspen wood chips) work better at limiting smells than others (like newspaper).
Rabbits don't smell as bad as cats, so just change the litter more often and the litter won't smell anymore.
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