the issue with serpent spawning is, if they spawn behind you, at night, during a storm, at max sail speed, with rain and waves, you might never see each other. the times you run into each other are a subset of the total spawns.

as for spawn rules - serpents can spawn during storms or at night, or both. night spawns despawn at day. storm spawns do not despawn.

when you occasionally encounter a sea serpent in clear skies and broad daylight, it means that it spawned a while ago in a storm, you didnt notice each other, and it stayed there until you finally saw it when passing by the same area again.

serpents will go back to their spawn point if they dont hit anything in 30 seconds. defensive retreat, to punish campers. you can let it hit your boat, or hit you, every 20-25 seconds or so to refresh the cooldown if you are trying to lure it to shore. so, it is worth marking serpent spawns in case it retreats, so you know where to look. once you kill it, you can remove the marker, as the spawn point only pertains to that specific serpent.