I think "на волну" might be approximately the same as "в разрез волне", i.e., "headed into the wave". Except the version with "в разрез" emphasizes above all the orientation, while "на волну" also means to get the ship up onto the wave, also called "scend" (= "подниматься на волну", according to the "Англо-русский словать по навигации..." и пр.). And then "по волне" means, more or less, to "ride" the wave, i.e., not to bounce up and down with each passing wave. Let's hope some marine experts come along, in case there are super-specific terms.

In any event, these are not opposites of "в разраз волне". That would be a "broadside" orientation to the waves (бортом, лагом), and I don't think that's a position preferred for making repairs.