The short tube coming from the hydraulic fluid reservoir (Power Steering Reservoir) is a vent and should be open and facing downward.
The vacuum lines vary slightly over the years and between tiptronic and manual. I'm not sure of the tube you are talking about without a picture or diagram. This may help: (from a 996)
Here's a 996 thread it was posted in and the discussion may help:
air intake/vacuum line routing - Pelican Parts Technical BBS
Our engines have basically the same vacuum set-up.