Comment 1 for bug 602767

Yes, it's a problem. The best fix would be for wrestool to not have to load the entire executable to find the icon itself, although I'm not familiar enough with wrestool to know if it's possible. See: https://bugs.launchpad.net/ubuntu/+source/icoutils/+bug/614918

Until that's fixed, a workaround would be to respect the Nautilus preferences checkbox you noted.