It's not quite as black and white as that as some games aren't compatible, such as skies of arcadia. That has issues with the vga box if i remember correctly.
but the problem with those games + vga is the compatibility issue of the vga output, not the 50 or 60hz question, right. In other words, if a game is compatible with vga, it shouldn't matter if it's 50 or 60hz, it should work just fine with vga, right?
Yes that is true. I didn't read the OP properly. I'm fairly sure the VGA box outputs at 60hz. I think the incompatibility arises from certain games not supporting a proper 60hz output.