The inertial dampeners work in sync with thrusters and subspace acceleration. The front of the ship also utilizes a rather powerful deflector shield. When a ship is not accelerating, whether traveling a steady pace or at a stand still, it isn't expected to move, and the deflector shield isn't on. The "shaking" is from the kinetic energy of the hard impact to the hull being dispersed. Given the amount of raw energy a beam weapon or torpedoes contain, the inertial dampeners are doing a good job of keeping everyone on the inside from becoming an instant liquid splat on the wall. The reason you hear explosions in space is because the sound you're experiencing is 3rd person perspective from a 1st person vantage point, i.e. that is what it would sound like if you were the ship itself. Sound travels within the ship because its made of matter, not vacuum.