I was annoyed by this bug so much that I attempted to make a script for it to add their spawns back, but while toying around with my pack (after doing what was recommended and regen the configs based on past reports and related issues) discovered that Structure Gel API has a nifty feature that allows me to visualise the borders of a structure (jigsaw segments, potential generation, structure boundaries, etc) and found the potential reason why this is happening.

Its because the spawn area for the Skelewags (being as large as they are) is too small for them to all the spawn checks in most circumstances (as there may be a RARE chance for one to spawn)

For a visual reference, here is a pillager outpost; the green represents the generated segments of the sctucture, blue representing part of the sctucture that could have generated (I think), and white being the area of the sctucture. I chose this because its a structure where pillagers will spawn within the white box.

This is the structure of a shipwreck

As you can see, the green and white bounds blend in, indicating they are the same size and because the sctrucute itself has a small area mostly occupied by blocks and how LARGE a Skelewag is, any attempt to spawn one in by the game naturally will fail primarily because some part of it would spawn within a block (which is also NOT water).

I have yet to test this in a pure instance to determine if another mod is possibly reducing the size of the structure for some reason or another.

(Note to those who are seeking answers: The Restricive Spawn setting for the Skelewag under Unique Spawning can be disabled in the config; however, it will not do anything UNTIL you restart the game for it to take effect (there really should be a message or (Restart Required) in the option description :/ )