The flaw is that a ship ten times as large doesn't necessarily take ten times the firepower.
For one, even assuming the firepower scaled, it might be the case that the attack on the sphere was overkill. If I shoot a puppy with a bazooka it will die. Does it therefore follow that to shoot an elephant a thousand times bigger than the puppy I need something a thousand times bigger than a bazooka? Of course not.
For another, as Seafort pointed out, ships tend to have explosive stuff in them. In World War II the Hood and the Bismark were two ships that were comparable in size and armament. Yet one salvo from Bismark sent Hood to the bottom. When Bismark was finally tracked down two battleships pounded her for well over an hour, firing more than 700 shells in the process, and she still didn't sink until a cruiser put a couple of torpedoes into her. With no ideas of what strengths and vulnerabilities Spheres and Cubes might have there's no real way to compare them.
Give a man a fire, and you keep him warm for a day. SET a man on fire, and you will keep him warm for the rest of his life...