Nuit:
Overworld sky directory: assets\nuit\sky\overworld\
End sky directory: assets\nuit\sky\the_end\
Delete the json file for the corresponding feature that you wish to remove.

Celestial:
Overworld sky: assets\celestial\sky\overworld\sky.json
End sky: assets\celestial\sky\the_end\sky.json
Nether sky: assets\celestial\sky\the_nether\sky.json
Open the json file, and delete the full quoted line along with the comma from "sky_objects", that you wish to remove.
(Make sure each sky object remains separated by a comma, otherwise the file will break. The last line must not have a comma after it!)

Biome dependant clouds:	can not be easily removed
Rain clouds:		sky 025 and 280-289 and 430-433
Snow clouds:		sky 024 and 270-279 and 426-429
Lightning strikes: 	sky 303-314 and 324-325
High altitude clouds:	can not be easily removed
Rainbow: 		sky 268
Iridescent clouds:	sky 330-332
Noctilucent clouds:	sky 328-329
Asperitas clouds:	sky 322-323
Mammatus clouds:	sky 318-319
Fiery sunsets:		sky 326-327
Sandstorm:		sky 026 and 290-299 and 434-437
Tornadoes:		sky 315-317
Supercell:		sky 333-334
Solar eclipse:		sky 401-440 and 507
Blood Moon / Blue Moon:	sky 011-014
Gas giants:		sky 004-005 and 405-406
Auroras:		sky 301-302
Northern star:		can not be removed
Shooting stars:		sky 029-032
Meteor shower:		sky 033-035
Black hole:		sky 003 and 404
Andromeda:		sky 002
Light pollution:	sky 006
Outer space:		sky 501-507
Hurricane:		sky 320-321 and 503
Main End sky:		sky 001
End highlands:		sky 002
End midlands:		sky 003
End barrens:		sky 004
Small End islands:	sky 005
End black hole:		sky 006-009 and 011-012
Red Nether sky:		sky 001
Cyan Nether sky:	sky 002
Brown Nether sky:	sky 003
High Nether sky:	sky 004