Weren't the Germans concerned about naval artillery destroying their fortifications because they were so close to the shore?
Yes, so they fortified the heck out of them as best they could. The examples of the Pacific campaign indicate just how overrated in terms of killing power Naval gunfire support could be against a prepared enemy. It happened that the Atlantic Wall was not yet completed, only a few months prior had focus changed to the Normandy area once the Calais area was suitably fortified, but the bunkers and whatnot which had been built would have required direct hits by large caliber rifles to be knocked out.
Ordinarily, one does prefer to have the main defensive line a bit behind the forward edge of battle to give a little reaction time, but assaults such as seaborne and airborne are a special case. It is preferable in such cases to engage the enemy before they have time to sort themselves out figure out where they are, and where their buddies are. Then keep them disorganized to prevent them from gaining an organized foothold, while you wait for your reaction forces to come along and push them off. However, Berlin did not authorize the release of those reaction forces when requested, which in hindsight was perhaps a bit of an error. As a result, having resilient weapons systems which could cover the beaches with direct fire was pretty much necessary.