would it be to much to ask that when the game encounters a resolution like 1024x2560 that it does something to cope and not cut the bottom of the screen off?

Must add a "you have 10 seconds to click I CAN SEE THIS button"

Probably. The only reason you'd be seeing a resolution like 1024x2560 would be because your graphics processor said it could handle it. If it can't, that's a fault of your vendor more than ours...

Do you have an example of what happens?

He's probably talking about the case where you run the game in linux with nVidia's twinview which says your dual monitor setup is actually one double width display. In the regular uplink at least this makes the game span the screens and the world map clips off the bottom so you can't click any buttons. I can't get onlink to run yet so I can't tell you if it has the same problem. Easily solved three ways:

1) Run Xnest to make a new X display, run uplink in it
2) Run a new Xserver with xgame
3) Run in 1280x1024 windowed mode, then use KDE's advanced windows properties to automatically take Uplink windows, remove the borders, and put it on the second screen. This method is my favorite because you get identical results to fullscreen but you can move windows on top and such without the anoying res change and you can click things on the first monitor without affecting your game. KDE's advanced window properties are amazing. So useful.