But for a user that legitimately wants to turn off images or javascript (why?), they won't want to see that message on every page. If the message only shows once then the problem the message was trying to avoid returns. If the message shows on every page legitimate users of the option are inconvenienced. Of course you could create yet another setting saying "Warn when I have obscure settings enabled"...
If the developers/designers of Firefox don't have a reasonably answer as to why a large enough amount of users would disable these settings, then they should be removed (or to avoid upsetting existing power user moved to about:config).
Users with images turned off by someone else wouldn't be confused if there was a yellow stripe across the top of the screen with a "you're viewing this website with images turned off [turn images on]" type message. Same goes for a "this page may display better with javascript enabled. [turn javascript on] if you trust this site" message for those browsing with javascript turned off.
Similarly, as the original post points out, the big issue with SSL is that you get a scary (and inaccurate and incomplete) message telling them to email the website owners because their site is broken, and not a simple message they'll need to "click here to turn SSL secure access back on" to view the web page.