Not really a stupid question, no...
The reason it happens is that you are dropping from great speed to normal speeds in an uncontrolled manner. Your ship will also take damage if you are forced to drop out of supercruise by getting too close to a star or an un-landable planet. If you want to test it, get up to faster than light speed then drop out by pressing your 'drop from supercruise' key twice for an emergency drop. You should take some damage there too.
It doesn't depend on the ship no. When you are at either end of an interdiction tether, unless the target submits, when you are wrenched out of supercruise then both interdictor and target will have a momentary loss of control, ship spinning and so on, and as above you will take some damage, and your FSD will take longer to cool down.