Naxreus' problem seems to be the problem with the map terrain edge hitbox effects; this has been a problem for all ships for a long time at certain map terrain locations; it affects all ships, but is definitely most noticeable with artillery cruisers.
To add to this discussion, other players and I have had recent issues with Storm Missiles being launched in-range at an enemy and absolutely no damage is dealt; they seem to disappear or not register hits at all when they should hit and do damage (before you ask, the targets aren't dreadnoughts or artillery cruisers with Armor Amplifer, or tactical cruisers with Emergency Lockdown).
Reportedly, according to the developer/publisher, larger ship parts even though they are bigger than the base ship model, do not affect a ship's "damage hitbox"; this could conceivably cause a ship to be "hit" but no damage to be dealt. However, Jawayne and I tested with friendly fire whether ship parts determine where a ship can land - it does affect this, but as it was friendly fire we were unable to test whether these hits would register damage - I therefore refer to this as the "shot hitbox". I wouldn't hold my breath expecting the developer/publisher to claim, even if it is actually the case, that ship parts actually affect the "damage hitbox" as that would deincentivize use, desire, and purchasing of different ship parts.