Questions

Thanks for the reply,
In other games that deals with layers, usually they would limit the layers to something that made sense, like 3 or 5 etc. And when swapping to a layer, the rest are faded out or completely out of view.
Some of your screenshots appear to show some of this actually.
As for warnings, the way Rimworld does it is via pop ups on the right side of the screen but I think you could expand on that to fit the theme.

From what I can imagine, a warning system could have the deck layer, say Deck 3, flash a certain colour code when events happen.
An example, take Simcity. That has Residential (Green), Commercial (Blue), Industrial (Yellow) and we add a new one, Alert!! (Red).
You could add a little text that explains the basics of what's happening.
Example Scenario:
The engine room is on fire on deck 3, the icon on the screen [3] blinks/glows red and the text reads, "Structure on Fire!",
Meanwhile, your ore processor has no more ore on deck 2, the [2] blinks/glows yellow with "No Ore" text,
Then, your food production is getting low also on deck 2, "Low Food". So the [2] now swaps from yellow to blue in cycle with the corresponding text.

And this will allow you to tap on the individual number to change to said decks and issue your orders.
With some testing, I bet this could be a great mechanic and would add a more immersive feel for those space junkies out there lol.

Thank you for taking the time to read,
CV.