Personally, I would go via Harwich - Hoek van Holland - evening to Harwich, sleep on the boat, train in the morning via Rotterdam is the timing worked out ... is the "Dutch Flyer" ticket still available for the middle segment (Liverpool Street to anywhere in the Netherlands) section of this journey?
Yes - see
http://www.stenaline.co.uk/ferry/rail-and-sail/holland/Where exactly are you making for?
If it's Brussels itself, then it's very difficult to beat the Eurostar for performance if not for price.
If you're heading for Antwerp and the like, then the Harwich ferry is worthwhile.
The trouble with the Calais crossing is that the onward connections aren't very good. Well, except for the idea of going to Calais Frethun and catching a Eurostar, which rather defeats the object.
The traditional ferry route ran to Ostend, where it linked straight on to the Belgian rail network - but I think that's only served by ferries from Ramsgate these days.