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Here's a better picture:

That wide area you're looking at in the center has to be disconnected and towed out of the harbor before something as large as an aircraft carrier can leave. Sure, small ships can pass underneath it fine, but when something as large as a naval vessel needs to pass through, that bridge has to be moved.

They don't bother moving the bridge ... the Navy parks its big ones (carriers are the only ones limited, just like they are the only ones limited by the panama Canal) at North Island, towards the ocean from the bridge.

South of the bridge, the commercial ships (if any were actually being built any more in S'Diego ...) from NASSCO are built to fit underneath, just like the LHA/LPH/LSD's as mentioned before. Theorectically, yes. (Then again, theorectically, you could use a buried nuke too there.)

Practically speaking, using enough megatons of conventional expolive to blow the sand away would be 100's (thousands ?) of times more than would enough to totally destroy any parts or pieces of the Coronado Bridge tha tare blocking the harbor.

So rather than blow up hundereds of feet of sand into a channel several hundered feet wide to get a channel 20-22 feet deep ... why not just blow up the little pieces of the bridge that are still sticking up out of the water?