I understand your feelings. I just went through the same thing (see
thread). I ended up paying just over $1000 to replace my 2009 hull with a 2014 hull. In the end I decided it was a reasonable conclusion because I did end up with a newer model of the boat.
I think from a boat owner's perspective, it is very frustrating because suddenly your expensive boat is either worthless or $1000 more expensive than the "next guy's" through no fault of your own. From Hobie's perspective, they have a very generous warranty program (both in-warranty and pro-rated). The pro-rated warranty I think is some acknowledgement on their part that the design (or manufacturing?) was not up to their standards, while at the same time saying you can't expect a boat to last for many years without problems. If you found the crack in the first two years I think they would have given you a free replacement. It is just added bad-luck you just hadn't used it for so long.
$1000 seems like a lot of money for a hull, but between the ~$200 shipping, the cost of the polyethylene, parts, labor, dealer time, taxes, it is probably around break-even for them. So it's not like they are trying to profit off the situation. Most companies would not even go this far.
I decided to pay the replacement cost because I knew I could then sell the boat for more than that to recover the cost if I wanted to (which I don't). Plus at least I got something positive out if it (newer model). Let's face it, boating is an expensive undertaking.