There’s actually an important distinction to be made here. Some of the GNIS feature classes (e.g. School) are archived. The records still exist and are readily available in the archived data set provided by USGS, but they haven’t been updated since 2021 at the latest.
Records in the archived classes are often much more out of date than that, though, because USGS didn’t do a good job of maintaining the data. So, you can still find these records and use them for reference. But you need to verify everything in them against more reliable current sources.
The only case where I would suggest deleting the gnis:feature_id tag is if the feature in question no longer exists, or if the current feature present in the real world is no longer the same thing as the corresponding GNIS record (e.g. a church no longer used as a place of worship).