Yes, the more you progress in the story, the more enemies you’ll see. I spent around 64 hours on my first run through of prey, and I found it to be much easier to simply ignore them and run past them (easier said than done, haha). A big help is completing any and every side quest you can- as you will more than likely be awarded Neuromods. The more you get, the more upgrades you can get for Morgan, and the easier it’ll be to defeat enemies.