All the command does is erase the resource from the map so it respawns. Some will respawn in the water, but some will respawn on land.
If I’m understanding things correctly, the water is being included in the potential ore spawn locations, and nodes that spawn on land are harvested and respawn in the water, out of reach. Eventually, all the nodes will respawn in the water. This command cleans them out so that they’ll respawn all over the map. It’s a short-term bandaid until the spawning can be properly limited to above-water locations (or garry introduces SCUBA gear–unlikely but a man can dream).
No reboot is needed. In fact, a reboot too quickly might not even be triggering a map save, which means that your clearing of the ores never even happened and the server loads from the save.