DVT is a very high profile 'in' condition which has been brought to the general public's attention only just relatively recently. Cases are now fairly media-hyped but in relation to the actual number of passengers flying, the risk of having a DVT is low. I refrain from putting figures incase they are inaccurate, but I think the figure was ROUGHLY one passenger suffering a DVT every six weeks of those passeners arriving into London Heathrow.
Flight deck seats have more leg room than economy seats as they can be moved backwards, and to the side in many cases. Pilots can use this facility to stretch their legs. They can also perform the same prevention mechanisms as passengers, including taking regular drinks of water (though it's often tea!) and even just getting up to go to the lavatory or taking a walk through the cabin if a flight is longhaul.
If you wish more information on this topic you could try the British Medical Journal website,
www.bmj.com, or do a search on PPRuNe as much information and opinion has been shed and shared on this site.
Regards,
FD