Using the new custom world generation options in 1.16 it is possible to have 256 tall nether in vanilla Minecraft. Unfortunately dynmap currently makes assumptions regarding the height of the nether here. This results in the upper half of the nether not being rendered at all.

In worlds.txt you can specify custom properties for each world. You need to specify a custom height of the nether map

Where is the custom height property documented?

this is what i have in custom-perspectives.txt

• class: org.dynmap.hdmap.IsoHDPerspective
  name: nether_top_map_hires
  maximumheight: 256
  minimumheight: 128
  inclination: 90
  scale: 16
  azimuth: 180
• class: org.dynmap.hdmap.IsoHDPerspective
  name: nether_top_map_surface_hires
  maximumheight: 256
  minimumheight: 128
  azimuth: 135
  inclination: 30
  scale: 16