In recent time I've noticed the Batcave is always incredibly clean, but inside the Batcave are living bats. How does Batman keep it clean from the guano ? or does Alfred work all the day cleaning the poo?
The extensive cave system underneath Wayne Manor is quite large. No doubt when Batman started placing equipments and lighting into the Batcave the bats were compelled to go deeper into the cave (or further from Batman's operations).
The various changes to the environment caused by the equipment, primarily noise and temperature, would have made for a less desirable living space for most of the bats. They just relocated to a different part of the caverns.
I recall once where Alfred became ill due to frequent exposure to bat guano.
There are other uses: