The Bug

Old buffet worlds that were generated using the caves or floating_islands generator do not generate strongholds anymore.
Ender eyes also do not locate strongholds that were already generated previously anymore.

How to reproduce

1. Go to 1.15 and generate a new buffet world using the caves or floating islands generator
2. /locate Stronghold
3. tp to the located stronghold
4. Open that world in 1.16
5. /locate stronghold
   → Nothing is found
6. Try to throw an ender eye
   → The ender eye entity does not appear

There are also 2 1.15 buffet worlds attached to this ticket with generated strongholds for easy reproducing.

Code Analysis

Inside the NoiseGeneratorSettings, the presets CAVES and FLOATING_ISLANDS are initialized with a constructor of StructureSettings, where the parameter generateStrongholds is set to false. This parameter is currently only set to true for OVERWORLD and AMPLIFIED.
Setting it to true here should be okay and not cause any side effects.
If a generator is used that does not have any overworld biomes, no strongholds will generate, since only overworld biomes support strongholds.

The parameter in question enables the special strongholds configuration.
In the JSON-fied version this equals to adding this inside of dimensions -> minecraft:overworld -> generator -> settings:

"structures": {
	"stronghold": {
		"distance": 32,
		"spread": 3,
		"count": 128
	}
}