If you only order the SSD, the 3.5" drive bay comes empty, but ready for a drive.
You can have, at most, three drives in a new iMac. One must be the SSD configured from the factory (unless you're willing to do some serious hacking, as you noticed,) one is the standard 3.5" hard drive bay, which you can order empty if you get the SSD, one is the optical drive, which is standard.
I suppose with some creative hacking, it should be possible to cram two 2.5" drives in the space of the 3.5" drive, but I don't think the motherboard has a fourth SATA port, so you wouldn't be able to use it along with the factory SSD.
Also, the optical drive is a notebook-size drive, so while it is wide and deep enough to replace with a 3.5" desktop hard drive, it is too thin. Even if you took out the optical, you could only fit a 2.5" drive in its space.