Today there is no software that could understand(well) that there are birds(or small planes) on the way that are going to be eaten by your engines, and damage it.
This is just fearmongering. Birds, sure, but airplane engines are designed to ingest small birds and for the most part can handle it reasonably well. Small planes still must have a transponder, and TCAS systems will identify and warn of ADS-B signals ("squawk"), even if the smaller plane has not been equipped with a TCAS transceiver.