I'm having a little trouble with this, as a former navigator (not on subs... but still...)
They were taking 15-minute interval soundings in open sea, with over 8,000 ft of water under the keel. When soundings didn't match the chart (and not by all that much) they periscoped to get a GPS position. Position checked out, and there was nothing proposing a hazard to the ship... so they resumed track.
I don't see here what they *should* have done that would have seemed reasonable given the facts at the time. Sure, if they'd taken a sounding in the few minutes before the crash they might have had something to act on, but I don't see where that sounding looked at all like it was needed?
The X.O. and the Navigator can kiss their careers goodbye...
Updating charts with the two year backlog of Notice to Mariners would have been a good place to start.