Realize that an explosion that would not destroy a ship from the outside could very well cripple or destroy it from within. The armor and superstructure of a ship is designed to withstand attacks from the outside not the inside.

Also you may have as much or more success by blowing the main armory of the ship. If you were able to blow the munitions (for example all the concussion missiles, proton torpedoes, mines, bombs) on the inside of the ship it would certainly be enough to kill the ship from the inside.