TL;DR: Just file bugs if necessary, and ignore the deprecation warnings for now. Unless it’s throwing errors, it’s not your problem.
Most likely, it’s indirectly depending on an out-of-date version of graceful-fs that depends on Node’s internal modules (even though it shouldn’t). That module by necessity does depend heavily on Node’s implementation details, but 4.x was written to be less brittle in that respect. Few things changed in the API between 3.x and 4.x.
For what it’s worth, one count a couple weeks ago had that module as the tenth most downloaded on npm. I don’t see that changing much. And because of the large use share of that module (npm itself indirectly depends on an outdated version), Node has already instated a temporary fix where they’re trying to get people off of the internal modules.
So don’t worry unless you get errors originating from it. I generally ignore those deprecation warnings, as they’re already very well known.