Minecraft wiki entry for Multiplayer_PvP_bases, associated text: Very difficult to start off with, meaning you will likely be transporting large quantities of items from another base.
Beds cannot be placed, as well as /home and /f home requiring you to be in the nether to work.
Generally little access to wood and traditional ores.
Ghasts can do a lot of damage to an unprepared base.
Zombified Piglins, or if it's big enough, ghasts can spawn in your base at any time.
Water cannot be directly placed, meaning that TNT can wreak havoc on your base!
Almost any player who comes will bring fire resistance potions, rendering fire and lava traps virtually useless.
It is difficult to activate beacons in the nether, as despite the fact that the beams can now penetrate bedrock, you will have to clear a lot of netherrack in order for the beam to reach the bedrock layer. Also, if you are unfortunate enough for a lot of netherrack to be completely encased in bedrock on the top (which is rather common) you'll have to build them a distance away.
Endermen might pick blocks off your base walls.