This is true of the merchant ships of most countries. The collection of all merchant ships bearing a nation's flag are collectively its merchant fleet.
Basically, this means that German flagged merchant ships are subject to German admiralty law when on the high seas, and that German merchant ships can be conscripted to aid a war effort on behalf of Germany in times of war. Stated another more direct way, this means that in exchange for the benefits of German sovereignty for a merchant ship owner, the merchant ship owner must sign up to be eligible to have his ship drafted into the German navy in times of war.
A U.S. specific description of the "merchant marine" can be found here, but the general concept that: "The Merchant Marine is the fleet of ships which carries imports and exports during peacetime and becomes a naval auxiliary during wartime to deliver troops and war materiel.", is equally applicable to the German Basic Law as used in this case.
A unitary merchant fleet is the naval equivalent of an "unorganized militia" or "selective service" made up of people eligible to be drafted, but who haven't actually be called up for military service.