Yes, you read it right, mSATA slot on this shuttle only runs at SATA II 3Gbps. The SATA III drives will work but only at SATA II speed.
You said you were going to put a HDD and a card reader into the case, so you only took 2 slots, there are 3 slots in total (2x3.5" and 1x5.25").
Take a look...