I'm new to Landies but very happy to own one at last! I've just bought a 2003 Freelander TD4. On inspection I found that the toolbox is sitting in a big puddle so I've drilled a drain hole. Being perhaps over fastidious, has anyone found any sort of valve to stop water coming back in should I decide to go paddling?

You should really ask about this well known phenomina in the Freelander section, but a quick answer is no such valve.
The water is getting in believe it or not because of splashing under the vehicle and entering through the seam around the "toolbox" well. The seam is spot welded instead of being seam welded. A good repair is to use 4 inch wide flash-banding from a building supplier to cover and seal around the edge.