Unity3D makes it easy to develop HoloLens apps. However, to be good at it, you need to spend some time examining its features.
Having .NET 4.x code in your app is very possible, but there are some hoops you have to jump through. You can use #if / #endif constructs or create a new set of DLLs, one for the editor, and one for the final app.
Performance in your app should always be on your mind. You can do a lot with the profiling tools in Unity3D and Visual Studio, but it is best to avoid having to deal with them. By using the tips and tricks I have shown you, you can get great results.
If you want to speed up the development time and do not mind the fact that you lose some flexibility, the HoloToolkit is a great way to start your HoloLens development. After all, now you know what happens inside of it all!