I don't think it should cause any major problems. While air pressure will keep the valve closed you will still probably lose pressure a little bit faster than if the valve was locked down. If you're pumping your tires before every ride you probably shouldn't have any problems.
That being said, if I was riding clinchers I would replace the tube as soon as possible. It sounds like you're on tubulars though so I would just try it out for awhile and see what happens.