For future reference, I've asked a friend of mine who is into canoe expeditions:

He ordered his collapsable kayak at unterwegs.ch in Aargau. Apparently they'll close the shop in September and move to Zurich next year. He bought a Feathercraft kayak (4000.- plus 3000.- for an extra hole and further customisation plus 800.- for paddles) which is still going strong after 1200 km. Another shop he recommends is globetrotter.de.

Other good brands, some of them focussing on other boats than collapsable canoes, are: Nautiraid, Klepper, Kahuna and Ally.