I understand that from the lore point of view it makes sense that the enemies blend in their surroundings, but from gameplay point of view it just feels like artificial difficulty. Cause I gave the game some more tries today and it's really hard to tell where the enemies and their bullets are, especially when you get a crew that has a big bonus to gems and the whole screen gets covered in them. I dunno, I would probably make enemy bullets a bright color(typical choice: red) and make gems a single color that's different from the color of bullets and bonuses(e.g: blue or green). And give enemies a white outline.
If you think that it's so important that the player is kept alert, maybe you could add crew members who have a passive ability of highlighting them? Or drones dedicated to that? And yes, I gave that cheat code a try, those drones are really useful(even if they tend to get stuck), not only due to their firepower but also the fact that they highlight their targets, which let me detect enemies that I wouldn't have noticed.