I've got grills on all three case fans and filters on the intakes. I've managed to clear the cabling well enough so that the fans don't contact them, but you're right, the idea was to use them to make sure.
It's currently only using the integrated graphics on the G3258, but I have been looking into using a PCIe extension to add a GPU in the future. The PCIe slot is currently tucked right behind the case fans at the bottom of the case, so I'll have to work on getting a solution sorted.
The motherboard is just a little MSI B85I and the storage is a HyperX 120GB SSD.