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The article says "a little more than 400 miles southeast of Guam"..."in an area where official Navy charts list 6,000 feet of water." But apparently the crew were still monitoring the depth of the ocean floor beneath them and not relying entirely on the chart.

IMO, it was a preventable accident. But like Prost1 said in post #5, I'm not a sailor or seaman either, but I agree with the list of questions he posted.

I am a sailor and a navigator, and this smells.
"But the investigation showed that there were at least five notices to mariners, most recently in 2002, about a large patch of muddy water about three miles south of the sea mount that were not incorporated on the charts the San Francisco was using at the time, the sources said."
Failure to ensure that notice to mariners are on your charts is a big no-no, but they were traveling south and this muddy patch had nothing to do with the accident. This is their most serious offense.
"On Feb. 5, for instance, the National Geospatial-Intelligence Agency, which produces map information for the military, issued a notice to mariners about the sea mount that the San Francisco hit."
This proves that the sea mount they struck was not on a prior notice to mariner, so they had no way of knowing it was there.
As to the depth, if you're going along at 500 ft, and the chart says 1000 fathoms and you're reading 800 fathoms, while it's a curiosity that is still 4800 feet deep, almost a mile below the keel. Charts are also pretty vague about precise depths at that depth. (sorry for the grammar) What really ticks me off, is that for under a $1000 you can buy a commercial GPS that gets it's updates off the internet and automates it without having to sort through pages and pages of notice to mariners. The same navigation system can actually warn you when your projected course (entered via waypoints) runs into objects that are known. It was a system failure, but the Navy has to have a scapegoat(s). (I'm ex-Navy).