I have a writeup on I2C here:
One I2C bus can support 119 devices. Any of them can be a master or slave, and you can broadcast. Of course they can't do that all at once, but there is provision for collision detection. If one is the master and sends a query and gets a reply, there should be no collision problems.
There is no extra hardware required (the hardware is built into the Arduino). The source is open, the required library comes with the IDE.
I thought that different baud rates would help me do the multiplexing, am I right?
No, I don't see how that helps in any way.
... the main receiver needs threads to listen to every single frequency.
I'm not sure what you mean by that. This is not consistent with:
I'm going to design it using a central node in charge of all the communications, that sends bits to one arduino and gets replies.
There are other design considerations, like the cable run length, how much data you have, and so on. Obviously if you have 60 devices all wanting to "talk at once" you may have problems, the issue is what sort of delay you can tolerate in servicing them.