The B-29 was certainly an inspiration to Frank Hampson. The 1954 Dan Dare Spacebook has a rocket with a front not unlike it. The late Keith Watson obviously copied the B-29 front for that 2003 piece of art from Spaceship Away.
I reckon the X40 is such a generic or traditional space ship shape that it will be difficult to pin down to any particular inspiration. But as you say, the cockpit may well owe something to WW2 aircraft.