But with SSL your root certificates change rarely and you can control them, as well as freeze certificates for specific websites. With Javascript code you don't have that kind of control and if you did it would require a massive change in the approach of creating a webapp in order to be managable.
It's not an insurmountable problem though, I would like to see an attempt at solving it (a browser extension would be required, but arguably you could have much greater transparency in updates than even most package managed apps if you used readable JS).
