Upon approach to the SF Bay, large ships are required to meet a pilot ship at the vicinity of the lightbucket or 'SF' buoy, about 16 nm from shore. A local pilot is then transported aboard and is responsible for piloting through the local waters. They must then stay in *very* clearly marked deep water channels while transiting the bay. However, this is not always foolproof, and not always because of dangers lurking beneath the surface. For example, apparently rocks were not the problem for this
I'd add that blowing up a few rocks in the SF Bay would be a ridiculous charade given that much of the bay is far too shallow to accomodate a large vessel. That is why there are deep water channels. It's like suggesting you cut down many of the trees close to the edge of a large throroughfare; the problem isn't the forest, it's keeping the cars on the road.