To some extent, but not necessarily
Usually, the positional relationship between two objects is understood because we know how the physics work. We know, for example, that waves crash down because of gravity, so the wave had to be higher than the boat at some point because we understand this basic aspect of physics. Onto works in your example because of this.
However, one could just as easily talk about a sticker stuck onto the bottom of a bottle or a child latching onto its parent's leg, etc. In these examples, onto is more accurately understood as "covering in some way" or being "against the outer surface."
Onto does not specify that the bottle was lifted and tilted so that the sticker could be applied or that the child ran laterally towards the parent before latching onto the leg. We understand that these actions had to occur because that is the normal way the child or sticker would be onto the bottle or leg.