I guess I’m used to compiling shaders but this really sounds like something is wrong. When I am recompiling shaders I typically just minimize UE4 and browse the internet, and its done within 10 minutes in a starter project. I can also just work without issue on the project in areas like Blueprints that don’t require material display. My system never gets so bogged down that I can’t do anything… For reference I am on an i7-6700k.
For complete projects it definitely takes a while but it depends on the amount of content you have but there are ways to optimize your shader permutation for your project.
As for why an empty project has 5k shaders, I believe this is just the engine content. Even without the starter content, there are still shaders that the engine needs to build. This should only need to be done once per project when you load it the first time or after an engine update so it is not something that should happen every time you load a project.