We've sailed from both Seattle and Vancouver and although we preferred Vancouver as the departure port, Seattle was fine too. We saw plenty of great scenery sailing outside Vancouver island.
There's always the risk of rough weather on either route. Getting to Hubbard Glacier and back can be quite choppy.
IMHO a must for first and maybe only Alaskan trip...Glacier Bay. It's stunning and better (and calmer) than the Hubbard trip. Hubbard's quite impressive in its own right. But Glacier Bay is tops.