Even though we've seen it running on the Steam Deck, until I bought one myself, I didn't know that Apolune 2 fails to launch on the Steam Deck OLED. This should be corrected now, since we've removed the Linux version from the Steam Store.
While the Linux version has been out for at least as long as the Windows version, it never worked fully. Linux savvy users were able to run the game by running it in the console, outside of the Steam launcher. I have been waiting for a very, very long time for YoyoGames to deal with this issue, and they have never gotten back to me despite numerous attempts to address the issue.
When the Steam Deck detects a Linux version, it will circumvent the Windows version and attempt to run the native Linux version. In the case of Apolune 2, for whatever reason, it failed to start, probably due to the issues with the Linux version. So, we have removed it, since it fails to start in the launcher which is required for Steam Deck use.