I mistakingly assumed something to be a bug. please delete.
If you're describing what I think you're describing, it's from one of your consoles, some kind of armor, IIRC. Right-click on the console, and there will be an option to disable visuals, just like on personal armor and kits. If it's not an armor console, check all the others.
I had a strange green hex pattern on one of my ships, too, and discovered accidentally that there was something with a "disable visuals" option in my ship's equipment/consoles that made it disappear when I selected the option.