This seems to always be the case for me. Any time I'm marinating a salad or pickling vegetables it always seems that the raw onion bite is very much diluted after soaking in vinegar. Is the vinegar 'cooking' the onions in a way, or are the offending chemicals water soluble and just dissolving into the liquid?
I expect it's just the water. Soaking in water, after at least cutting the base off the onion to expose the core, is commonly recommended as a way to reduce the potency of onions to avoid crying. It should also reduce the potency of the flavor. If you're giving it enough time to marinate or pickle, the effect will be even larger than the shorter soaks people use to try to avoid crying.
Edit: I'm not sure how thoroughly you're marinating and pickling, but very generally, adding one strong flavor tends to reduce our perception of others, so you may also have some effects just because you're tasting the vinegar.