First, the "shorted out" layout is suboptimal. The design idea behind the USBLC6-2SC6's pinout is forcing the signal to flow into the chip at one end, and flow out of the chip at another end. There is no connection from input to output on the circuit board, it's bridged by the chip itself. If you externally short the pins, the high-speed ESD energy will take the path of least inductance and partially bypass the chip, reducing its effectiveness. To maximize its ESD protection, I would use two additional jumpers resistors to create a bridged connection across USBLC6-2SC6, instead of shorting it.
On the other hand, a circuit board "flow through" routing is found in the pinouts of many other ESD protection chips with acceptable performance, so it's probably not a really big deal and it's not strictly necessary. So do whatever you like with my information.
BTW, as a fan of old-school schematics, I dislike the default KiCad symbol of this chip, the drawing makes it almost impossible to show the natural signal flow so I happened to have another symbol at hand. Feel free to use it.