I'm from the U.S. and I've been a visitor in Canada for almost six months. I was planning on going up to Hyder, AK and from there traveling around Alaska for a couple weeks before returning home (to the lower 48). I have no wish to overstay in Canada. However, as there is no U.S. border presence at Hyder, would I experience a problem with Canada thinking I had never left?
I'd be more concerned with the US not knowing you'd entered. Even at the border near Vancouver, there's no actual Canadian exit, you just pass the Canadian border and enter through US immigration - they want to know you've entered.
In This is Me by Danny Wilks, who I know from Vancouver, he kayaked from Vancouver to Alaska. He had a problem where he arrived in Alaska, tired, and went to register with the border at the next town the next day. I forget the exact details, but basically it was a case of "you've been here illegally for a day???" and he was deported.
Naturally this is not something you want to happen, and as a US citizen you're probably not going to get deported, but you may get in trouble for not registering your return to the States. I'd recommend stopping at the Canadian Customs office that pnuts suggested, and that way you can do two things - firstly, make sure there's nothing extra they need from you, and secondly, to check with them if they need to notify the US. Put the onus on them and that way if it is your deed to achieve, they're likely to help you out with a phone call or whatever may be required.
Please do come back and let us know how it goes, sounds like a good trip in an amazing part of the world!
Canada does not record the departure of US citizens, but assumes that you left in a timely fashion (same as the US does for Canadians). The only time an overstay would be recorded would be if you got caught in the country for whatever reason by police.
But how do you propose to visit the rest of Alaska from Hyder? The Alaska Marine Highway ended ferry service to Hyder back in 2001, the only way in & out of Hyder is via Canada.