Whether to use encryption is a per-room setting, not per-server. It’s controlled by the person who creates the room, not the server admin. It’s on by default, and cannot be switched off later.
Rooms can be created without it because that makes sense for large public rooms, like those migrating from IRC, where privacy would defeat the purpose.
This is misleading. Matrix respects the e2ee setting that you choose when creating a room, and it’s enabled by default.