Additional info from @Matt_Bradock

What I deducted from thorough testing and info from other players, the pirate reinforcement wave can spawn anywhere in the 3x3x3 sector cube with the station in the middle. The problem is, that you don't have vision to all those, you have vision only to 7 sectors out of that 27, because what you see is the sector you're in, and the 6 that share a side with yours. You don't see into sectors situated diagonally to yours. There is only 25.9% chance that the pirate wave spawns in a sector you have vision and sensors coverage in - which is why you usually don't see the pirates: they have spawned in one of those diagonal sectors and the best way to find them is to check the corners of that 3x3x3 sector cube surrounding the pirate station. At least, that seems to work for me. Check the upper corners first as they are more likely to spawn there.
/initiate_wave works because that command always spawns the baddies in the same sector you're in. Station attack triggering pirate spawns used to work the same until the wave customization update. What would certainly solve the matter is making only the 6 sectors adjacent to the pirate station, and the station's sector itself eligible for spawning the pirate wave. Thus, they'd always show up on your nav.

This could be a good trail to fix it.
To my knowledge the sectors loaded around a player were always 3x3x3 but if this changed, this would be the cause for the spawning to drop the pirates in unloaded areas.

in addition to the placement issues noted above, i am noticing that regardless of the ship i am in, only an "/initiate_wave 1 1 -1" equivalent group of reinforcements is ever spawned in.

is it possible to confirm or deny that currently the only pirate ships that spawn do so as a result of a pirate station's distress call? i am no longer seeing any loose pirates anywhere in the universe (despite having a full set of 10 AI waves installed), but see nothing to this effect in the changelog published alongside the wave designer.

i would be keen to follow-up on this particular issue as i am trying to design some fun, naturally occurring, and variable pirate action for players, but it is hard to know what to report on a feature i am unsure of the design and intent behind. i don't entirely know what "working" is supposed to look like for pirate spawns anymore.

You can test it easily in single player.

Create a new world and set as default.
Start the game.
Add a wave with 1 Isanth for Faction -1 and difficulty 1.
Spawn a battleship and get in.
Jump to undiscovered stations till you find a pirate station and attack it.
After 10 distress calls, look with "/search Isanth" for the spawned amount of Isanth around. I don't think you will find 10.
Wait till the come to you..... or not.

Last tested with 0.19446 and a sector size of 5 km.

Update, the fleets spawn now but they don't immediately fly to you. It can take 2 minutes to half an hour till they reach you.

Apparently everything was fine in 0.19361, but not since 0.19400

I started my test again with version 0.19478. With 6 calls 4 Isanth Type-Zero Mm were spawned. Only the first and nearest wave 0-0 came to my position, but this is the same behavior like before. The other disappeared when I used search command again? See screenshot. I jumped to the position of wave 3-0 and it was there and attacked me.

I started a second try. With 3 calls 3 Isanth (6-0, 7-0, 8-0) were spawned. After 12 minutes they were still in the same sector.