If you look around, it is discussed frequently. First, sailing out of Vancouver, you get to sail east of Vancouver Island, what some call the "true" Inside Passage. Very scenic. Seattle sailings go to the open ocean west of Vancouver Island.
Second, with a couple rare exceptions, you can only sail roundtrip cruises out of Seattle. Out of Vancouver you can sail one way Vancouver to Seward or Whittier, (or back), which opens up more locations and scenery, plus more land options when you get off the ship in Seward or Whittier.