You can now block other empires from messaging you in-game.
There is a new “Block Empire” button on the message page that you can use if you would like to stop receiving messages from another specific empire.
If you block them, they will see something like below if they try to message you:
The block works both ways, so if you block them you will also not be able to send them a message either.
Messaging as a whole will likely be redesigned at some point, but for now this works well enough to empower players to control their own communication, so that staff can focus on other priorities.