So... luck of the sea is reducing my chances to get neptune's bounty, and all of the other chests? Because pretty much the first thing I did when I picked up this mod was enchant my fishing pole to catch all of the treasure and I have yet to catch anything, despite catching vanilla treasures.

src/main/resources/data/aquaculture/loot_tables/gameplay/fishing/junk.json

I read about this in several places (reddit, etc.), so it seems to be a known issue, yet I didn't see any issues here (open or closed) that have mentioned this? Is this... intentional?

Switched from a gold hook to a diamond one and switched to a pole without luck. Immediately caught a goldfish and box, after hours of trying with luck last night. I don't quite understand how the bounty itself is implemented, but it seems weird to me that the treasure chests are considered junk.

You're reading outdated information. Neptunium items were considered junk in Aquaculture 1 (1.12 and below). In Aquaculture 2 (1.14 and above) they are considered treasure.

The reason that they were considered junk in earlier versions is because it was a workaround, I don't remember to what. However as of version 2, you will have better chances of fishing them if you use a fishing rock with luck of the sea.

If you read though the loottable that you linked you will see that there are no Neptunium items listed in it.

Okay, I get that for the case of neptunium, but what about the treasure chests? Why are those marked as junk?

Huh. I don't actually know. This is a @Shadowclaimer question.

To not lower the chances of getting vanilla treasure. We get plenty of complaints regarding that already.