Depth is not your problem.
Shuttles have the AGP slot on the outside of the board (closest to the case) and as such do NOT have the room for a double height heatsink on a graphics card.
My SN41G2 (IGP version of the SN45) has to use single hight cards (ones that could have a PCI card in the slot next to the AGP card).
AFAIK, most nVidia gaming cards need to use a double height heatsink, best bet is to ask the supplier if you could fit a card into PCI slot 1 with the card fitted, if they say no then you cant fit it in the SN45.
I went for an All In Wounder 9700pro but I know the 9800pro works & the low profile X800 also works with the newer 250w PSU's