I cant guarantee I will be able to fix it but I will try. I just wanted to see if you would actually put the work into it. I kind of tricked you, its usually next to impossible to fix a game without having it installed. Which I have no idea how that works with a mod since they don't have access to that.
When we fix a game we change the games shader code. Thats a bit strange to me and may not even be possible. Ive never tried to fix something thats a mod nor has helix. If you cant find either I cant help at all, sorry.
If you can only find the pixelshader I cant help you. I will take file and see if I can figure it out. If its a vertexshader and its seperated from rest of the hud(by itself, it should dissapear or distort). Cycle through vertexshaders and see if you can find it. We wont be removing the texture that clips (at the top) unless we have to. I cant gaurantee it will work but it will require effort on your part.
I will see if perhaps together we can find a solution. Then there are the problems with fixing a game, updates that break fixes, DLC, etc. Lots of time goes into fixing each issue and the amount of people who would benefit are just too small. I know helix wouldnt fix it for the mod, sorry. I havent actually played X3 since Im not really into those types of games but perhaps I can help. (This is not helix, helix has been busy with work so I will be answering)