Yes, thinking about stuff like this can certainly put a damper on how we view "beauty" in the world. Again, I know how you feel. We sound very similar. I also often turn to nature for comfort for similar reasons. When considering ideas like the sim theory, one can't help but to feel as though any sort of spirituality, wonder, or mysticism is completely wiped away and replaced with a bunch of 1's and 0's. This is what really had me down when I originally made this post.
Again, I don't have the answers, but I can do my best based off of the thought processes that have personally helped me overcome this obsession.
First and foremost, as I mentioned before, everything is still up for debate. Look at String Theory. The worlds smartest scientists are debating this theory now, some claiming to have solid proof while others criticize it. Some scientists believe it is the only current theory that provides a good explanation of "everything", while others quite literally call the theory a failure. This shows that even a popular theory, discussed by geniuses who claim to have very convincing data, is criticized and still possibly...incorrect. In comparison, the Simulation Theory simply began as a thought experiment, and is still only really seriously studied by a handful of people (from what I have gathered from my research, at least). Even if people claim that they have found convincing evidence, there will always be criticism and opposing opinions. What am I getting at here? If you view the Simulation Theory as a bad thing, there will basically always be hope that it's incorrect.
I think the keyword here is perspective. When I find myself asking questions like "is this real" or "what IS reality", I stop myself and try to put myself back into MY perspective. If you think too small, you become obsessed with what we're made out of. Is everything really made up of nothing but tiny vibrating string-like things? Are we just a bunch of 1's and 0's like in a computer program? Suddenly you don't see things as they are. A bird stops being a bird and is just a mass of cells and bones. Trees stop being beautiful and become tiny particles that simply make up what we perceive as trees. That sort of takes all the "magic" away from life, doesn't it?
But...that's not the perspective that we are meant to see it in. Our human brains are meant to see things from our perspective and nothing else. Anything outside of it, we simply cannot comprehend. It doesn't make any sense to us, and therefore it scares us. Does that mean that nothing is real, and our perspective is just an illusion? No! Maybe there IS a deeper meaning to all of this, but when we look at it in the wrong perspective...we're missing it.
Think of it as going to a movie theater and pressing your face right up against the giant screen. The movie wouldn't make any sense at all. It would just be a bunch of chaotic, flashing colors whizzing by your field of vision. Does that make what's going on in the movie any less real? Again, no! All the chaotic flashes of color you see are all part of the bigger picture. They have a purpose, and that purpose is to make the movie happen. As you back away from the screen, it makes more and more sense until you can see it at the proper perspective, where it makes you cry, laugh, and feel countless other emotions.
My point is, while life as we know it may be made of unimaginably tiny things (vibrating strings, 1's and 0's, etc) that makes us feel like it's not "real", that doesn't mean it isn't real to us. That doesn't mean that there's no purpose. It all HAS to be made out of something, what does it matter what it's made out of? Regardless of what the building blocks of nature are, you cannot deny the impact it has on you. We are connected to it somehow.
So what IS reality? That is something that is probably impossible to answer outside of our perspective, but we can reason what reality is to US. Towering mountains give us butterflies in our stomach. Lush forests with sunbeams leaking through the treetops make us feel serene. It doesn't matter what they're made of, what matters is the impact it has on us.
This leaves you with a choice. For some reason (unfathomable by us humans), we are here, experiencing what we know as life for a limited amount of time. You can spend that limited time obsessing over why we are here and what is real, or you can focus on what you know and find enjoyment in what is here. Will you watch the movie with your face pressed up against the screen, or will you sit in the audience?