You misunderstand. I meant that a simple shuttle having a warp accident and smashing into a planet would most likely devastate it. Accidents can wipe out planetary populations..., so it'd make sense for proper Starfleet vessels to have immense armament compared to what we see as militarily appropriate through the eyes of today.
The energy has to go somewhere. As it's not transmitted to the surrounding space when entering and exiting warp, it's a decent assumption that it's stored as KE as the vessel moves at warp. There's no mention of mass alteration and time dilation during warp, so we can probably assume that the mass of the vessel is the same.