Well, suspension helps the tyres track the road, by letting the wheels move up and down semi-independently of the rest of the bike. This helps to keep the contact patch of the tyres more constant than if the tyres are deforming to do the same job.
This makes a suspended bike hold the road better, and return greater rolling efficiency than than rigid. However this comes with a downside (a bit like cake!) in that the action of pedaling will cause the suspension to react, which decreases the transfer of energy from the rider to the road.
Well set up suspension on an upright bike will still suffer these inefficiency losses, though they are minimised by seperating high and low speed damping a la Fox's Propedal, and Specialized The Brain systems - they are still more inefficient than rigid though.
On a recumbum, pedaling force is pretty much horizontal, and the suspension acts in the vertical plane, meaning that as the two forces are separated, the rider doesn't lose energy throught the reactionary oscillation (?) of the suspension - as they barely create any!