Arduino Yun, node.js and serial
Autosolved thanks to this old forum post.

It is Serial1 not Serial.
In the Arduino code in the Yun Serial is a different object from Serial1. Even if it is not super well document (or at least not in the first dumb google search) here are some links that talks about Serial1:

https://www.arduino.cc/en/Tutorial/YunSerialTerminal
http://andrea-toscano.com/arduino-yun-tcpip-to-serial1-redirect/
http://crossbar.io/iotcookbook/Arduino-Yun-Disable-Bridge/