The North Sea cycle route has been shortened, and now bypasses Belgium and France. Also the website is out of date, showing a non existent ferry route. The North Sea route followed the Den Helder to Boulogne route LF1 for that section with an optional tee off to Calais. This route was well surfaced but poorly signposted in France and Belgium, and also went inland taking the picturesque rather than direct route.
I can't recall any problems cycling Calais - Zeebrugge direct, just pick up a map at Zeebrugge and keep the sea on your right and south west on your compass. It might be worth going inland to avoid Dunkirk which can be a bit messy to get through without forward planning. All well surfaced, but Belgian signposting is probably not the best in Europe.