I think were talking about the same device which I circled in red. You may well be correct that the base of that device sees manifold vacuum. If so, then having the one port capped off is no issue.
However, I thought the device was a thermostatic switch that is mounted in the engine to sense it's temperature, and the base of the switch is not open to the manifold vacuum. Thus manifold vacuum comes into the switch via the port that is capped off, and when the temperature is right the switch opens allowing that vacuum to go to the vsv, etc.
Easy enough to check, just pull those hoses off of the valve when the engine is running and see if there is vacuum present on either of the 2 ports when there are no hoses connected.
Randy Rosetta KDØKWX TLCA #19351 NOW 2015 Rubicon Hard Rock & (2) 1970 Boss 302 Mustang's THEN 69 FJ40 Buggy "Meanie", Mini-truck "Gecko" & 74 FJ40 "Blue Mule"