Convoy Repopulation
 

I've noticed a couple instances wherein I sank ships in a convoy, only to have them respawn at the convoy's origin and race back into line. They also seem to be strangely focused; I was terrified to have a destroyer come running up on me out of nowhere, but it passed within a few hundred yards without so much as blinking his light (it was daylight, clear, surfaced). Has anyone else noticed this?

As always, much depends on mods, but this isn't typical or correct behavior.
Ships spawn when they enter the contact zone of your best equipment all through the game. You may not realize it unless you notice game lag, as your crew will only call out contacts based on their values/equipment they currently have. If you spawn a group and sink ships or damage them, they shouldn't reappear while in the contact zone. However, it you let them escape the contact zone and despawn and later respawn them, ships you sunk will reappear in the group. You're basically starting over with each despawning.

If you're saying a DD passed you while you were on the surface in clear daylight only a few hundred yards, something is wrong. Even in stock seems it was 3000 yards. With mods like TMO, about 10,000 yards

I'm thinking the DD not spotting you is weather related....

Occasionally I notice the crew with their rain gear on and it's a sunny day with clear skies, or something similar. Re-setting the weather fixes these issues after a few game-time hours....

I usually give SH4 a day after this reset for the weather to settle back down to normal cycles and the lower time compression used while in enemy waters. Anyway, there are issues with the SH4 weather, mostly after a long period of high time compression.

The AI may have believed it was a thick fog with zero visibility day, I can't think of any other reason why the DD wouldn't be able to see you.

Happy Hunting!