Preventing users from teleporting on top of the nether?

There's a relatively simple command block solution to this, which works in vanilla.

First, set up a scoreboard objective to detect players in the Nether

/scoreboard objectives add onNetherCeiling dummy

Create a clock (I suggest using a fill clock) in your spawnchunks (so that it is always loaded), hidden in a box of Bedrock, and add the following three command blocks, to be run in this order:

/scoreboard players set @a onNetherCeiling 0
/scoreboard players set @a[m=0,y=127,dy=128] onNetherCeiling 1 {Dimension:-1}
/effect @a[score_onNetherCeiling_min=1] 20 1 2 false

The first two commands will assign a score of 1 to every player in survival mode (m=0), in dimension -1 (the Nether), with a y coordinate between 127 and 255.

The last command will hit the evildoers with 1 second of Wither II. You can do whatever you want here instead, just use @a[score_onNetherCeiling_min=1] as your target and it works. If you prefer smiting them for their insolence, try

/execute @a[score_onNetherCeiling_min=1] ~ ~ ~ summon LightningBolt ~ ~ ~

There is a slight chance that this won't work with Bukkit/Spigot though, due to the way Bukkit treats the alternate dimensions. Assuming that does not affect NBT data (and I don't see any reason for that), you can place the command blocks on top of the Nether ceiling instead, but you will have to make sure the chunk they are in stays loaded.

Rather than changing a lot of blocks, consider this:

To complete the teleport exploit I believe you need to have a 1 block between you and the nether roof, so if you make it so there is none of that, they can't teleport.

So you can either make it so there are no 1 block gaps (design 2), or you can make it completely solid (design 1).

You could use a Worldedit to fill up the space above for all the allowed space in the nether with bedrock, so when they teleport up, they suffocate and learn that doing that is not allowed.

That would take a long time to do, that's like 50 billion blocks. Using a rig with 128GB ram dedicated to the server, twin/triple/quad 2080TI cards, the best cpu on the market it would still crash trying to place that many blocks. Even doing 50 million blocks at a time would take you a long time to place that many. There's tons of plugins that prevent building above the nether ceiling and give ceiling void damage. For instance, I use this on my server: https://dev.bukkit.org/projects/no-above-nether?gameCategorySlug=bukkit-plugins&projectID=263893

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You could use a Worldedit to fill up the space above for all the allowed space in the nether with bedrock, so when they teleport up, they suffocate and learn that doing that is not allowed.