Complex sentence: In many of these cases, the purpose of these treatments is ambiguous and there is dispute whether many were anti-fouling techniques or along with lead and wood sheathing instead intended to combat wood boring shipworms.
Split into simpler sentences: In many of these cases, the purpose of these treatments is ambiguous. There is dispute whether many of these treatments were actual anti-fouling techniques, or whether, when they were used in conjunction with lead and wood sheathing, they were simply intended to combat wood-boring shipworms.