At first let’s understand how subsonic Cruise missile poses a threat to naval ships. Naval vessels are mostly very slow like snail compared to aircrafts & it moves on the surface of ocean slowly with long range early warning system & air defence missiles, guns & other decoy system to prevent enemy strikes.
As you know “earth is not flat” which is why the radio waves actually go upwards after 15-20km. This is how, Horizon creates problems for the naval ships to detect low flying objects from long distance.
Subsonic cruise missiles are developed to take advantage of this limitation caused by the horizon. It flys low which makes it difficult to be detected by the radars. The target ship with it’s radar only can detect the missile at the range of about 15-20km. Now the target ship can only engage the missile with quick reaction surface to air missile or CIWS.
Nowadays the missiles have evolved further. To protect itself from CIWS or short range ADS, modern cruise missiles like Russian Kalibr are supersonic & increase it’s terminal speed to mach 3. So in terminal stage the missile becomes so fast that target ship does not get enough time to activate it’s air defence.