According to the changelog for version 6.5.0, "Backported all changes from Apotheosis 7.1.0 through Apotheosis 7.3.3."
One change, the pufferfish recipe, is present.

However, the two new shelves, the Seashelf of Aquatic Filtration and the Deepshelf of Arcane Treasures, are not present.

Were these two shelves supposed to appear, or is it intended that they were not ported?

Interesting. I just looked at the repo, and there is no recipe in the 1.19 branch for the filtering shelf. Also, when I searched JEI for the filtering shelf earlier, it didn't pop up.

Well, no, the filtering shelf cannot be backported as it relies on vanilla code which is not present in 1.19 (the Chiseled Bookshelf). The other two pieces that you mention are missing (the pufferfish recipe and the treasure shelf) should have been added (but based on @SiverDX's comment they were omitted)

Well, the pufferfish recipe was added, hence the first screenshot in the issue, so you don't need to worry about that.

aren't those based on chiseled bookshelves

Only the filtering shelf is, the treasure shelf is just a static shelf that flips on treasure enchantments

The pufferfish recipe was added as to make crafting seashelves not so annoying in modpacks that add other fish to the fishing pool (since obtaining one can become virtually impossible when this happens)