Did the gunboat fire over its own crew?

Was the gun firing over the crew?

No. The object under the firing line is a flagstaff. The later comment concerns sailors' familiarity with nearby gunfire.

The gun in the displayed photograph fires over a flagstaff, while the sailors are elsewhere on deck. The visible crew and gun mounts also provide a sense of the vessel's size. Naval personnel become accustomed to nearby gunfire through experience. Infantry unfamiliar with heavy artillery can react very differently to guns firing close to them.