What are Prefabs
The Unity Documentation for Prefabs simply describes it as
A template from which you can create new object instances in the scene. Any edits made to a prefab asset are immediately reflected in all instances produced from it but you can also override components and settings for each instance individually.
How does it effects performance
My experience tells, it does not. Since google does not point to any rigid analysis that whether or not prefabs improve performance nor I have done any experimentation regarding this, this Unity answers.com question explains it like this:
There's nothing magic about prefabs; they are simply a convenience. There's no performance difference between putting two cubes in a scene, or making a prefab out of the cube and then putting two cube prefabs in the scene.
That's all. If there is any performance improvement reports or analysis or anything regarding this, I might want to know about it as well.
Thank you.
EDIT:
I tried what you said, made a terrain of 50k by 50k with heightmap resolution of 512 (couldn't get any higher).
- Pressed play button first ~ 5seconds
- Pressed play button second time ~ 4-5 Seconds(roughly)
- Prefabbed it and pressed Play ~ 4-5 Seconds
- Waited for a while, may be 5minutes and pressed play 2-3 seconds
Time difference was not significant but here's what I noticed.
Whenever you change Terrain settings, on the bottom right corner, there is some processing happening. If you let that complete, the startup time would decrease.
Here's what it looks like:

I didn't know your terrain settings and how complex it was but from this I can deduce that bottom-right processing might be the thing that manages the load time. It might be loading in the memory and could be doing some one-time calculations/ processing.