Not all software is under your direct control. Once business processes achieve a stable working state, it is imperative that they maintain uptime, sometimes in excess of six-sigma uptime.
Imagine your business is NASA. Are you going to let mission systems auto-update 18 secs before launch?
You can choose to neglect paying on your debt for some period of time, but it always comes back, more expensive, later. Case in point: the IT leaders that refused to upgrade from Windows XP and Server 2003 are now paying astronomical prices for "extended support" and "migration/rehosting." If they would have simply invested in maintenance to ensure compatibility with newer OS/browser combinations, they would not have this problem.
Pay now, or pay much much more later. Tech debt is a huge problem in IT, and ignoring it won't make it go away.
Also, is it 100% true that they dont update software on actuve systems mid mission?
What if they discover a critical bug?
What they don't do is allow updates to happen automatically. They're carefully pre-tested, and the update is carefully planned and scheduled. Their goal, like most enterprises, is to minimize risk, and bugs that you know about and understand the impact of are much less risky than updated software you haven't been able to test yet.
The Universe auto updates. So you need to update your rover when that happens.