It's an interesting question. Zubat is undeniably based on living bats, which are mammalian. But canonically all Pokémon lay eggs, and that's not something I'd like to contradict in my writing. So what do we do?
Fortunately, in this particular case it's not too hard to find a biological workaround.
Even though there are no bats that lay eggs, there are mammals that do. Monotremes like the Platypus and the Echidna are living mammals that lay eggs, and there's evidence in the fossil records that large varieties of egg-laying mammals like them once dominated much of the land mass that now comprises Australia.
In the full PokéNatomy book I have a section on eggs, their purpose, composition, and evolution that clarifies this a bit. Suffice it to say, that mammals definitely can lay eggs and in the Pokémon world this seems to be the norm rather than the exception.