How do I deal with a joist in the way of where I need to run a pipe?
My answer is to cut your two inch hole as close to your drywall as possible.  In the picture you went right down the middle and barely hit the joist.  Methinks that you could drill right along the side and have to barely notch out the joist below.  Might not even have to notch all the way through it.  No reason for vac lines to have to be centered in your wall.  Use the notch guidelines I found to help further.


Notches in floor joists may occur in the top or bottom of the member but may not be located in the middle third of the span.
A notch may not exceed one-sixth of the depth of the joist except at the very end where it may be one-fourth of the joist depth.
The length of joist notches cannot exceed one-third of the depth of the member.
Holes bored in joists must not be larger than one-third the depth of the joists. 
Holes cannot be located within two inches of the top or bottom edge of the member, or to any other hole located in the member.
Holes cannot be located within 2" of any notch. 


Below is a helpful chart that provides actual notch and hole size limitations for 2x4, 2x6, 2x8, 2x10 and 2x12 joists. It should be noted that limitations on the allowable notching and boring of wood joist are meant to retain the structural and functional integrity of the member.