Ground planes disposition in Ethernet connection
However, I have the following doubt about it: If the common mode
  currents circulated in the shield and the system GND plane is not
  connected directly to it, there maybe will some voltage bounce between
  these them. Could it lead to intensification of the electromagnetic
  emissions?


A ferrite bead does not isolate high voltage as the question suggests, it blocks high frequency. In an ESD event this can block short term high frequency voltages, but it can only filter and there will be current flowing across the ferrite. Ferrite won't have "bouncing" as much as a regular inductor because ferrous material has hysteresis and loss and does not form and RLC Q point like a regular inductor would. 


  The use of transformers /chokes to block common mode currents is very
  common in design guides for Ethernet physical layer, but is not that
  common to USB physical layer design guides? Can I use the same
  filtering/isolation methodology to USB connection? Would it be a good
  choice?


Chokes can be used for USB but are generally not recommended for reasons stated in the link. I've never found a good use for them. If there is noise that needs to be filtered out, then use one (like RF noise). So, no don't use a common mode choke unless there is a reason to (you have issues with noise in your eye diagram). TVS diodes or other filtering can be used to shunt potential currents away from electronics with USB. The shield should also be tied to appropriate points (like chassis ground) to shunt ESD currents away from electronics.