By cluster with 3 nodes, you mean a 3 node replica set? You can take down and restart nodes with minimal impact on the replica set - it's part of the purpose of replica sets. For minimum impact, shutdown nodes with
db.shutdownServer() and use
rs.stepDown() on the primary before restarting it. Do one node at a time so a majority is always available and there should be minimal impact on the operation of the replica set.
-Will