It is not malice, it's laziness and stupidity. Most apps are so trivial it is absolutely not necessary to break compatibility when you release a new version.
Depending on the app, it's just sound security. On a jailbroken device, you cannot assume any of the OS safeguards are still in place. On a stock iOS device, there's pretty much no relevant malware that could be on that device. On a jailbroken device, all bets are off.