A quick google turned up http://www.cdnn.info/industry/i041228c/i041228c.html article that says the sea-floor may have shifted up and down by up to 60 feet, but doesn't say if it would be permanent. It also says it may have a small, but noticeable effect on land far away. From what I understand, a powerful earthquake on the San Andreas fault involves a shift of just a few feet - rememeber though, a continent moving 5 feet requires the release of a truly massive amount of energy.
Regarding ocean-floor mapping - it has only recently become possible to have really accurate maps of the ocean floor. Typically, within a few miles of shore, you'll have a depth reading every 100 m or so. Out in the open ocean, they can be 10 km apart. It would seem to me that this sub, if operating that close to the bottom, should have had better charts, but that's a lot of land-area to chart and it shouldn't be too surprising that that's the best we have.
One of my profs at the Naval Academy was an officer onboard a sub that ran-aground for this exact same reason (uncharted seamount), which pretty much ended his career. The picture painted by the article is of a cliff - that's not generally how they work. Usually, its just a few degrees of rise over many miles. One thing that's not clear to me yet - the sub may not have had its depth-sounder turned on, which is apparently common for military subs because it makes noise.
edit: a little more - googling shows some people speculating that this was a collision, not a grounding. Apparently, the water was supposed to be much too deep for even an uncharted seamount. My prof said that his sub had dents in it that no one was allowed to talk about, but everyone was proud of...
