Yes, you're right, that's the whole point. A surface vessel rides on top of the wave and gets bounced around. A sub can go below the disturbance; even in a wave of great amplitude, once the sub is well submerged, it's not subject to the same 'roiling' as a surface vessel is.
I grew up on the New England coast and am far from an experienced mariner, but I have been out at sea daily (usually no more than 35 - 50 miles) and know what you're saying. Incidentally, I worked at Portsmouth Naval Shipyard for a while and was on the boats every day while they were overhauled. Some of my more 'lubberly' colleagues would ask some of the submariners about this very point. Most often, they stated they would rather be in the sub and safe below, than on top, in a storm.
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