On the box of the storm trooper case, it says that it supports m-atx, atx and xl-atx mobos. Since e- atx is in between atx and xl-atx in size, would the storm trooper support e-atx mobos also?
Not necessarily, there's no guarantee since E-ATX has some different mounting holes than ATX and XL-ATX.
I'm guessing since your looking at the box you'v already bought it? Check the mounting hole positions and see if the board will mount anyway. I suspect at worst you'l be missing two mounting holes at the very bottom of the board, the ATX mounting points should also apply to E-ATX.
E-ATX would still use the same mounting holes as an ATX. And why would it be missing mounting holes at the very bottom? It's the same height as an ATX.
Oops, my mistake. You will be missing mounting holes on the far right of the board.
However, as I said before your probably fine. All the ATX mounting points will be usable, just the E-ATX specific ones wont be supported.