Baking soda is fine, although I’d choose an acid to neutralise rabbit pee smells and stains. Rabbit urine is quite alkaline (up to pH 8,8 😯 ) because it’s concentrated and has a lot of ammonium compounds. That’s why bunny pee really stinks when exposed to air for a while: the compounds fall apart and release ammonia gas. We always clean urine stains with unscented cleaning vinegar in a spray bottle, because it removes the smell and the colour. I’d always use unscented products with rabbits around, because they have very sensitive airways.
You can also clean with lemon or lime juice if you want a natural cleaning agent. One little caveat: I wouldn’t use lemon/lime juice on fabrics, because our bunny started to lick and dig at the spot. It probably smelled like a tasty fruit treat to him. It should be fine for cleaning and deodorising the litter box though. Lemons/limes also make a great descaling agent to remove pesky calcium stains in the kitchen and shower. You can also descale the kettle with it without having to worry about vinegary tea. I make my own cleaning agents because they’re a lot healthier for both of us than the heavily perfumed bottles from the shop. Vinegar and lemon juice for calcium stains and odours, rubbing alcohol and soda crystals for greasy stains.