Yes, spalling alone would have reduced the command efficiency to 'bout nil. "Deathtraps: The Story of an Armored Division", though not Civil War and certainly not naval, covers the subject from the viewpoint of a fellow in charge of cleaning up the aftermath of same. (M4 vs. Flak 88)

The fellows who unloaded their Mortars on the forts of the lower Mississippi, for the most part, had never fired a Mortar before training at Key West on their way to Ship Island to stage for the run up the river. Farragut had signed off on fuzes of too long a burning duration from the Washington Naval Yard (18 sec.). Many were duds and the ones that burned to their full duration were far into the muddy ground when they exploded. The Bureau of Hydrology had a survey crew plot the positions and targets to the foot, hardly the kind of shooting on the fly that a vessel to vessel action would entail. Those Yankees had it down pat by the time the last rounds were fired at targets in Florida, I can assure you.

Time and operational experience, an ongoing assessment of mission would have made Confederate Mortar practice effective. Emphasis was placed on rifles for operations, a mistake to me. Federal Mortar crews had land targets with a strategic objective. Confederate Mortar crews, waterborn, by virtue of the defensive goals, would have had the Federal Navy as its target.