Unlike a lot of imported IDs, a GNIS feature ID has meaning on its own. The GNIS feature ID is the only permanent ID that every federal government agency uses to refer to a populated place, and it’s the primary ID used for natural features, hence its inclusion in the NHD import.
Mappers do go around manually adding gnis:feature_id to features by looking them up in GNIS. This isn’t discouraged as far as I know. Especially for natural features, GNIS can be a good source of names (as the official national gazetteer), so the GNIS feature ID acts as a citation for the name. That said, the GNIS feature ID may become less important over time as Wikidata imports more of GNIS and we continue to link features to Wikidata.
For reference, here’s an Ohsome API chronology of all the popular GNIS feature ID keys. This is just a raw count of elements, not unique values:
