No full size phantom that I know of has a window.
The 410 is not really "Small" its a mid tower, which is the most commonly used tower size for computer builds. The Phantom is huge, the 410 is normal. As far as watercooling, I dont know about the 410, I own the full size Phantom. It includes mounting hardware and the space up top where the fans are is large enough to house a big Corsair H100 should you have the desire to, thats where it would go.
Yes the full size Phantom has 2 hard drive cages, the main one has 5 bays, the one in the middle has 2, and it is removable. I believe its 4 or 6 screws that hold it in place. I removed it to store the unused wires from my PSU.
How long of a graphics card can it take? There is none that wouldn't fit in a full size phantom. The case is large enough to handle a big Extended ATX mobo. Which one would I go with? The full size, its only $20 bucks more, why not?