The Silencer

The Silencer can be considered a relatively 'humanitarian' type of Weapon of Mass Destruction [WMD] since it was made to disarm and shut down ships... system-wide. It is essentially an Electro Magnetic Pulse generator of apocalyptical proportions, that has to be loaded for a long time before it can be fired.
There is no known way of protecting a ship or an installation from Silencer's effect. Every single electronic component system-wide will require being replaced after it is fired... which, unfortunately, includes the one installed on the ship that carries it. It is a weapon that's hard to use properly and costly - not only because of the damage to itself (the Silencer itself is unnafected, but its ship...), but also because it is guaranteed to knock out the ships guarding it during the loading period.
On the other hand, most warships deserving of the name are designed so that replacing even all of its components aside from the hull (the most expensive part) is possible and can be done relatively fast (depending on the size of the ship). Meaning that Silencer can be used to knock out entire enemy fleet that is then captured by friendly units that awaited for the right moment to strike in the Hyperspace... and can be pressed into service.