I had this problem as well, I almost quit Aquanox 2, but I found a...way around the crash. As far as I know, there are no known fixes to this crash. However you can cheat your way through it. Go to the aquanox 2 GOG shortcut on your desktop (if you don't have one on your desktop, open A2's files and select the shortcut from there) and click on properties. Then go to Target, and at the end of the message already in the Target, type: -drake -strega -amitab -fuzzyhead -mice
Save your changes to the properties and go into Aquanox 2. Go in game to the hells vortex mission and press F11. This will make it so you automatically complete the mission and can activate autopilot. You'll get the default mission rewards as well.
I know this isn't a "fix" per say, but its the only way I can find to get around the crash.