One way to deodorize shoes is to coat the insides with baking powder and place them in the freezer (inside a sealed bag) for at least 8 hours. As a base, baking soda neutralizes bad odors, which are often acidic. The freezer kills the bacteria that are creating the smell, so even if you do not have any baking soda, the freezer can help prevent odors.
If you don't want to coat the inside of the boot with baking soda, you can place it in a cup, paper towel, or coffee filter, and it still absorbs odors. Another way to make boots smell better is to use items that both absorb the smell and add a fresh scent.
For instance, you can leave orange peels in the boots overnight or dab a bit of vanilla on a piece of balled-up newspaper to leave in each shoe. The newspaper absorbs smells even without an added scent. Kitty litter can also absorb bad smells; most commercial litters are designed to neutralize odors to keep them from infiltrating your house.
Another solution is to use cheap vodka or rubbing alcohol. Lightly coat the inside of the boots with the alcohol by using a spray bottle. Like the freezer, the alcohol helps to kill the bacteria causing the smell.