I personally would not want to spend a month or so in a C Dory 16 doing SE from Prince Rupert. Looking a bit longer range at the economics, if you can swing buying a 22 or 25 you will far more comfortable. If you buy a 22 keep it a couple of years, and then sell it, the chances are that you will have "lost" little if any money. But have gained a fantastic experience. (we have even run into folks "cruising" in a 13 foot whaler, and of course several doing Seattle to Skagway in Kayaks. So the "seaworthyness" issue is not really an issue if you watch your weather. This last summer we only sat out 1 day because of weather in SE AK, and one day tucked behind a trawler when it got rough, and allowed him to knock the waves down, so we could maintain 7 to 8 knots.
We have cruised in that area a total of 6 summers, and never had a concern about water--there are many ways of conservation--especially in a small boat--about all you really need is for drinking and a few gallon jugs or 5 gallon cans will get you by if careful. We have cruised almost every charted area, and a few uncharted areas along the way. This last summer in the C Dory 25, we went from Petersburg, to Pybus, then to Ford Terror, and to Juneau and had plenty of fuel for the trip--which was close to 200 miles, with our few detours along the way.
We did explore Dundas Bay this year for the first time, but had been into Glacier twice before. We found that cruise ships are there for only short times--and that with an extension you can get 2 weeks in Glacier Bay, and thus explore all parts.
I don't see any difference in Customs on either side of the border in the last 20 years, except that on the US side, they seem to want to see a video of the passports or report in person--but occasionally we had to report in person in the past.
My biggest concern in any really small boat, is the cramped area for "living" especially if you cannot spend much time ashore. The issues in SE include the high tidal ranges, the bears, the cold weather and water.
I have used CQR, Delta and Manason Supreme anchors, all with excellent success.