I checked around the military sites and it seems that the line to the air cleaner was for the underwater fording. So when the motor diaphragm sucked in air it pulled it from the sealed up air cleaner system. I read in a few spots that it apparently never worked well and later model 50's era Military vehicles stopped using the extra hose.

This was interesting about a restriction in the vacuum line to the distributor/wiper motor tee,

From g503.com:
Apparently the tee at the junction of the vacuum supply from the vac pump/vacuum to the wipers/tube from the distributor has a reducer, being a .040 constriction in the center part of the tee from the ignitor- this is to keep the vacuum flow from the distributor down a bit, so the vacuum to the wipers is still good. The way I chose to do this (not having the original tee, regrettably) was to put JB Weld in the reducer fitting to the copper line to the ignitor (the line from the vacuum pump, & to the wiper motors is 1/4", the center of the tee to the distributor is reduced to 3/16") and when fully cured I drilled a hole in the JB Weld with an .040 drill bit. Others have used other methods but that seemed an easy way to do it.