Others have commented on why the acquisition makes strategic sense from a technological perspective, but I think it's also important to consider how it makes strategic sense from a psychological perspective. For a long time, devs loved bagging on Microsoft. I once saw some Microsoft guys demo something cool at a conference, and they had to basically apologize that they were from Microsoft, because dev sentiment toward the organization was so negative, even though they were doing cool stuff.

The acquisition of GitHub was absolutely intended to capture a tool/ecosystem that developers liked using and benefit from that positive sentiment. That's why Microsoft has been so cautious about branding GitHub as a Microsoft property out the gate. It's trying to ease devs into the idea that the company is something devs can like, and I wouldn't be surprised if this psychological strategy is at work with the npm acquisition, too.