The stern was so designed to reduce drag but was insufficienly armoured.
Actually the stern except for the most aft rounded section, which detached, was well armoured. The armour was the reason the very end section eventually detached. The very round end was a modular section added on, but the ship building protocols at the time of construction forbad welding directly to armoured bulkheads. Therefore attachment pieces were riveted to the bulkhead and the distal stern section was fillet welded to the attachment pieces. This was good design as far as was known at the time, because it would mean that for the welds to fail; several inches of each fillet weld would need be fractured. It was not known until the 1990s that shock waves can cause fillet welds to fail by deformation of the parent metal plates.
Prinz Eugen later in war had stern section blown off by British Submarine torpedo.
There's nothing unusual about this. Large torpedoes typically blew off stern sections, and bow sections, of cruisers during WWII.