No, the ocean is not fully mapped. It's written in the article: "With only one-quarter of the sea floor mapped with sonar, it is impossible to know how many seamounts exist."
In the specific case of the San Francisco, because notations indicating a probable seamount were not transferred from other charts when the chart being used was compiled; there is some lack of clarity on how much the failures involved are the responsibility of the command crew of the sub and how much of higher command, but its definitely a failure to appropriately use existing information, not a “the information did not exist” problem.
While the area was apparently not well charted, the responsible crew not using the information at hand (including information as to the the quality of charting data for the area) was also apparently at play in the Connecticut grounding.
How could it not be in the chart though? Is the ocean not fully mapped?