Why not? Scabbed joints can be incredibly strong. You see them all over the place... steel bridge construction, house framing... if you use the right material and correct fasteners, the joint can be as strong or stronger than the original material. Granted, the joints are not as pretty or elegant as scarf or lap joints, but for belwo decks, I don't think that would be a concern. Moreover, if the structure is being joined to existing structure, making a scarf or lap joint could be pretty tricky, especially if one end of the stringer is glassed to the boat.
Now, if you're talking about slapping a 2x4 across the joint and nailing it to the butted stringer pieces, I'd have to agree with you... but that would be a poor repair.