They're called renewable because it's possible to do them in a renewable manner. Specifically, the energy in them comes from the sun, in a fairly short time span (i.e. years, rather than millennia or longer). So the original energy source is renewable, and the route from original source to usable power is short.
It is also possible to do them in a non-renewable manner.
Nitrogen fertilizers don't have to be produced from fossil fuels. They are currently, but they don't have to be. There are renewable alternatives.
Using biofuels doesn't remove any of the essential elements (phosphorus, potassium) etc from their respective cycles. They're still around in the biosphere. This is most easily visible if the route is from biomass to biogas to energy; in that case, the solid matter left over after the extraction of the biogas (carbon and hydrogen) has all the nutrients, and can feed the next generation of biomass.