Just learning my way around commerce. Just spent a bunch of time following official instructions that told me I needed to set up a department. 

I finally figured out that support was deprecated. So does that mean that I just remove the support link from the menu manager and move on?

 

It will exist through the 4.x series but it will not exist in the 5.0 series.  So it’s up to you to decide if you want to use it for whatever time you remain in the 4.x versions. If you add it, just realize it will be gone later and you’ll have to figure out something else at that time. When you deal with the pain is up to you.