Not sure what is going on here but I have narrowed it down to Natura and sponge together. Wither skeletons will not spawn when both are installed. Seems to be they may get replaced by zombie pigman?

Just to add more confusion, were having the same problem on Horizons 3 server, which doesn't have natura installed.

Blaze spawners still work with sponge+natura.

Removal of sponge makes everything spawn properly again, also seems blaze get replaced by zombie pigman.