A few minor corrections for how you call things. Your “Die()” is a method. You dont instantiate methods, you call methods. Prefabs are premade gameobject setups which you store in your project hierarchy. You can instantiate prefabs to turn them into actual gameobjects, which show up in the scene hierarchy ingame. You are not checking the y-Position of your player prefab. That would never change! You are (correctly) checking the position of your player gameobject.
Just to clarify what Prefabs are: Unity - Manual: Prefabs
As was already mentioned: small checks such as this wont affect your performance. You could have thousands like it, and would not notice. As a rule of thumb, especially as a beginner: do not worry about performance. This will slow your development to a crawl and take the fun out of it. If you ever stumble into an actual performance problem you can trace it to the correct culprit using the unity profiler, and then fix that specifically. Unless you know what you are doing, 99.5% of potential performance problems you think about and try to optimize wouldnt have ever become a problem in the first place, thus wasting your time. Performance is an advanced topic, but as modern hardware is orders of magnitudes stronger than it would have to be for most games, you dont really have to care too much 
Since i mentioned, here are the profiler links: Unity - Manual: Profiler overview
(But you dont need to look to deep into it for now, just know that it exists to help you)
As for understanding Unity, the easiest overview is this chart:
It tells you how everything Unity does is connected, and when what is executed. It may seem a bit overwhelming at first, but if you ever wonder, for example, when Awake() or Start() are actually called, or how the Update loop works, or when Collisions are actually checked, then this chart shows it all.
Other than that, if you ever wonder about the actual Unity API, check the documentation. The Unity documentation is one of Unitys strongest advantages. It’s really, really well done.
For example, you can search for things like “Vector3”, “Transform” or “Collision” and get a full overview of all involved properties, functions, and oftentimes some programming examples and a list of connected topics. This gives you a full overview of how these things can be used, and what they are even capable of doing in the first place.
However, while the documentation is amazing, it is more for specific topics. It wont teach you how to program or what to do in Unity, or the broader picture in general. If you are still very much at the beginning of your journey, i recommend the C# + Unity programming tutorial series by Sebastian Lague on youtube. He starts at absolutely 0 knowledge and builds form there, with what i find to be very intuitive mental models.