Ignoring players is handled by the NerdMessage plugin.
When NerdMessage deals with a player, it uses an "NMUser" object, which contains a set of strings of the usernames of players that are being ignored. The NMUser objects do not persist through restarts, the plugin creates a new one the first time it interacts with a player, and keeps a list of these objects in memory.
So in order to persist through restarts, the plugin would have to write the lists of ignored players to disk, and probably store them as UUIDs instead of player name strings. It's not a huge amount of coding by any means, but it's not as simple as changing a config value.
This kind of problem arises because nerd insists on "rolling their own" plugins or CH scripts for everything, instead of using one of the hundreds of open-source chat plugins available, which have more features, allow easier customization, and require less Tech Admin time and effort. This is one reason among many why Nerd is less "nimble" in making changes and trying out new ideas.