Vertical flows are more efficient with everything else being equal. The reason for this is due to the number of passages the charge air has to go through. A vertical flow will have twice as many passages as a horizontal flow core(when comparing a 24"X12" core).
Due to the inherent greater cross sectional area, while retaining equal volume, the velocity of air through a vertical flow intercooler is half that of a horizontal flow. The air spends the same amount of time in the intercooler, although it only travels half the distance. Half the distance traveled through a restriction = less pressure drop and more power. Also since the air charge spends the same time traveling have the distance, its going half the velocity. This lower velocity helps reduce pressure drop.
Derivation for Flow in a Pipe:
A = Cross-sectional Area of Pipe (SI: m2)
v = Velocity of the fluid in the pipe (SI: m/s)
Thats the thing, the motor is ingesting a set amount of air regardless of intercooler design. It is only flowing that set amount. With equal volume cores, it takes the the same amount of time for set amount of air to pass through the core.
Regards,
Justin