The mongod process can generate startup warnings under a number of scenarios (running as root, read-ahead values not optimal, THP enabled, _id index missing).
These warnings appear both in the mongod.log logfile, as well as at the mongo shell prompt each time you login. (It's the second of these which this ticket concerns).
However, these warnings are static - that is, they will not disappear even if the original condition is resolved, until the mongod process is restarted.
Whilst some of these warnings refer to situations that would not change without a mongod restart anyway (e.g. read-ahead settings), others refer to situations that may be transient or that could have already been resolved (e.g. missing _id index, or THP settings).
mongod should provide some mechanism to acknowledge/suppress or clear a warning for a condition that the user already knows has already been resolved, so that it would not appear on each subsequent mongo login.