I love Vancouver and sailing from there, but Seattle is more logistically convenient for American citizens cruising to Alaska. You certainly must still clear customs after your cruise having sailed into foreign territory, but it's much easier to handle customs for a single ship at the Seattle pier that it is at the Vancouver pier and the airport with passengers at times from several ships being processed simultaneously.
Think of it this way, when you fly to Vancouver, you clear customs arriving into Canada; you sail back into America and then clear customs after your cruise returning into Canada once more; and then you clear customs yet again at the airport to return into the States. Not to mention, round-trip flights in and out of Seattle are often less expensive than those in and out of Vancouver. I'm sure Disney recognizes the logistical benefits for its passengers sailing from Seattle.