I have two SSD in the 5.25 bays. The first one is mounted in a 2.5 to 3.5 to 5.25 tray =). The second one at the bottom is just held in by some 3M removable double Velcro adhesive tape. In the future I plan on buying a 5.25 tray that can hold dual 2.5 drives and then spin them around to hide the cables. Just need the 5.25 tray and some right angle power cables.
Without side fans installed the NH-D14 fits perfectly. It appears that the bottom side fan would fit just fine. But you are correct, it doesn't look like the top fan mount on the side panel would have enough room for a 25mm thick fan. Maybe a thinner one though.