I think they split into two pipes just after the turbo so that two pipes go out the engine bay (out both the original send and return holes of the factory cooler) and into the new cooler. From a flow viewpoint, i can't see that splitting it can be any better than one single pipe.
When you split it so close to the turbo, the air effectively fills double the volume, which (when fluid expands to fill a void) will cause a pressure drop. So now we have less pressure (but more flow) along two pipes, with added turbulence at the split (remember this is why when we have a separate wastegate dump we join it back to the exhaust a fair way down from the turbine so there is no turbulence). Compare this to the pressurised flow of a single pipe - higher pressure, but no disturbed flow or turbulence until it reaches the intercooler.
So when the two pipes reach the intercooler, the flow does not have to distribute itself as much inside the end tanks, and it should in theory flow much more distributed across the IC core. However, this is where fluid flow research is at its best - i am sure that HKS, TRUST et al have done hours of flow testing to ensure their endtanks distribute flow evenly across the intercooler core. Many companies both local and in japan believe that this is the key to a cooler that flows well, cools well and does not restrict flow too much - end tank design. So now the single pipe IC has reached the cooler, and if the endtank is designed correctly the air will distribute across the core (with a fair amount of turbulence. This pressure drop and turbulence will occur with both styles of cooler.
So the charge of air passes through the core at a lower pressure and is collected at the other endtank, reducing the volume (to outlet pipe volume) and hence re-pressurising the air. Now what i am saying is a well designed twin entry should perform as well as a single entry cooler, but there is more scope for variation. This system would work better for a very big turbo, as it will keep pressures up and air flow speed up in the twin pipes before the cooler.