You are correct NH3/4 will build up during the Nitrogen cycle process but it will be consumed by NO2 and convert to NO3 as the end process. To help turn your soil you add things like springtails. This will help reduce the likes of tiny NO2 pockets much the way a fish tank is I imagine. they will also help clean up during the process when things like leaf litter and poo is decomposing as part of the cycle and over time will turn into good soil.

I fully recommend the bioactive approach to soil, the cleaning will be spot cleaning mostly.