I assume the laptop SATA drives have smaller connectors
Nope. Same connectors, same configuration.
OK thanks. Even the power connector? Still a nightmare connector and adapter wise inside an empeg box.
Assuming the bridge chips are easy enough to get hold of, a small PCB could be designed to plug directly in to the empeg header and have a short power and short SATA cable to the drive (maybe limited to a single drive). The connectors sticking out from the drive would probably cause the most problems since they'd probably hit the display board and I've never seen a right angle SATA connector...
NB: All of this was thought of without even looking at an empeg or measuring anything.