Without Blackholes you do not get Anti-matter, without nebulas elerium, without these resources you cannot build many ship and planet improvements.
So, with the exception of BHs & Nebs being a pain to navigate around why would you want to get rid of them?
First of all, I buy whatever I need from the Galactic Bazaar.
Second, I have been playing this game for a long time and, while they were interesting to me at first, I find Black Holes, Nebulas, and Asteroids to be annoying to navigate around and detract from my enjoyment of exploration, expansion, developing worlds, designing and building ships, and engaging the AI in battle. Therefore, I was happy to see that the devs gave players the option to exclude them from the game and disappointed to see that their implementation did not do what it said it did. It is not the end of the world, but it is another example of something the devs need to fix: either get rid of them completely when you say "None" or change the label to say "1" when you move the slider all the way to the right. I recommend the first option because, if the player wants none, they should be able to play the game with none.
Third, the reason I play the early release versions and post things I find here is that I really love the basic design of the game and want to do what little I can to contribute to making it better. I am not just a crabby old retired programmer complaining just to hear the sound of my own voice, I am trying to give you feedback so that you can improve the game.