If you wish to understand what is going on in your thaumcraft pipe netowrk you need to make the essentia resonator - the "fork" thing. Tapping it on pipes will tell you the pipes suction (and current essentia if any).
Your problem is simply, while directional pipes block the propogation of suction in a direction through themselves they do not add their own suction.
The simplest thing to do would be to add a label to the jar you want to fill.
For bonus points you would craft an essentia buffer and a few bellows - you can configure the sides of a buffer using a want to have zero, 1 or "full" suction, and full suction is 32x the number of attached bellows. Attaching bellows to a buffer and configuring one side for full suction will allow the buffer to pump essentia out of a jar attached on that side, and if a different side is configured for zero suction, a jar attached to that side will be able to fill itself from the buffer.