There was a bug in TA prior to 2.x where the autodesigner didn't take miniaturization into account, but that should be fixed.
60 attack on a tiny isn't that monstrous near the end of the tech tree, and there are no single guns that give +60 attack, so that can't be what you're saying.
Ships don't require additional engine modules/sensor modules/etc to move, see other ships, and so on...the hull has basic values for these, and the racial stats of your civ further increase them.
If your complaint is that ships with all weapons have more firepower than ships that have engines, etc on them, keep in mind that engined ships generally have more flexibility due to their maneuverability. However valid a complaint it may be, the game is not able to be that realistic.
If your complaint is that endgame all-weapon ships have no defense, that is unfortunately a part of the game's mechanics. There are marginal counters to it, including the defense modules in TA, as well as swarms of tiny ships (as each gun can only target one ship per round), but by and large end-tree all-weapons is the way to go (although the cost is excessive).