Set in the 22nd century CE, space explorations reached maturity and the farthest human colony is on one of the moon of Neptune. So far the only voice from space that we have heard comes is our own, meaning the search for extraterrestrial intelligent life continues. Every nation still don't trust each other and race to occupy as many territories of space within the solar system as possible, current trend in designing spacecraft is to have a self destruct mechanism built in. Is there any political reason for every spacecraft manufacturers to install such a dangerous protocol or device on their products?
Spaceships would be very valuable in the empty expanse of space. They likely wouldn't just be instruments of war, they would also be one of the primary resources that parties would be willing to fight over. By adopting a doctrine of self-destruction you can discourage enemy parties from trying to usurp control of your ships. This could be instrumental in discouraging aggression from piratical frontier groups.
Now perhaps your enemies are content with just blowing your ships up anyway; why bother with a kill switch? Well, space travel is a seriously complex problem and the solutions to that problem would be valuable intellectual property. Having a self-destruct option would prevent your technology from being studied by your enemies.
Finally, you can force the crew's obedience to their faction who holds the self-destruct codes. It would probably be prohibitively expensive and take too long to send a another ship to intercept and reign in deserters.
Unless the nature of politics has changed drastically, in the 22nd terrorism is still a problem, and a hijacked interplanetary spaceship would be an extremely effective weapon for such purposes.
A self-destruct mechanism would make sense as a last resort to prevent a 9/11 on a grand scale.