Silver,
Maplin sands (north coast) is about 1 fathom over a large area, and Margate sands (south shore) is about 2 fathoms over an even wider area. I may have Silver Island too far north, and thus dropping the northerly two runways into the main channel, which would not be a good idea - in which case the island may need to drift south a little, or put the domestic runways on the south side.
Maplin Sands is to the east of Southend, so you would need to park your island just off the coast, and I think you would have just enough space for 2 wide spaced parallels, running roughly NE-SW, but I wouldn't like to see local reaction to such a proposal. Margate is well to the east, so you might aswell use Manston and give Iran Air some company. If you log on to Ordnance Survey, you can see the locations of these sand banks.
I don't even know why we are debating this subject, because building on land reclaimed with sand is a known technique.
I don't think the Dutch polders are comparable, the Zuiderzee is shallower and surely calmer, being an inlet and behind coastal islands.
Combining projects might lower some costs, but only if the location for each is optimal in the same location. The barrage you mention is merely a report, I don't think there has been that much investigation into the matter, or a costing of such a mammoth undertaking.
Any barrage to the east of the major ports could not be crossed by simply placing a bridge on top - the structure would have to be very much higher to enable ships to pass under, then you would have the challenge of what you would do with a road and railway crossing at height, then needing to dip to avoid conflict with the runways. The Oresund crossing, situated near CPH airport, uses a combination of bridge and tunnel, but there is no barrage. I think that is why Foster's answer puts the road and rail link through a tunnel. This would be much more expensive further out, especially if the surface is uneven.
Would need to see a cross-section of the estuary at this point, which I don't think either of us have easy access to, but this is part of the fundamental problem with building here - it is both expensive, and risky. If it wasn't, all the house builders in the country would have been trying it long ago, not just the flashy show off builders in Dubai, where they have (or had) the money.
As I said before, the sand needs to be stabilised and contained (preferably within a concrete wall)
Such a structure and wall would also need to be high enough so the site was above the tides, and that is quite some volume on the 6 runway site you propose.