From official canon (not including stuff from Disco), we don't know exactly why the Nomads' decided to wage war on Humanity, or weather their intentions were a war of anihallation, or simply downsizing the population and taking control of what's left for their own uses (i suspect the latter).
What we know is that the Nomads were, while 'technoligically' superior, no match for humanity (based on the latter's numbers, their ability to manufacture war machines en masse as opposed to 'growing' them, and the simple aggressive and ingenious nature). So, the Nomads would simply take control of as much as they could, using humanity's factions against one another. Once this is done, they would either 1: assuming they had the numbers, infest the whole of humanity, or 2: infest the leaders of the houses, and ensure their status quo over time.
As time went on, they'd use humans as vehicles for their own purposes, whatever those may be. Integrating human technology, infrastructure, and biology with their own. So, instead of wiping out humanity, they'd be made their slaves.
The simple logic of 'why destroy something you can use?' would apply.
Although, the above scenario ignores the storyline of the Discovery mod, but I doubt in either case, the Nomads would go through all the trouble to eradicate humanity without taking advantage of their ease of manipulation and various useful attributes to their own ends.
