Should probably remove the display of disabled options, but I think the minor edit notifications are also disabled.

Per bug 19468 the options *are* removed when actually disabled...

The "(disabled)" text here is not due to features being disabled, but rather because someone physically added that text to the labels in July 2009:
http://prototype.wikimedia.org/rc-en/index.php?title=MediaWiki:Tog-enotifusertalkpages&action=history
http://prototype.wikimedia.org/rc-en/index.php?title=MediaWiki:Tog-enotifwatchlistpages&action=history

In a quick test, I can confirm that I'm not receiving notification emails when I have another account edit either my user talk page or a watched page, regardless of major/minor.

Based on what should be the running code, if the config options are in fact disabled, they won't show up in prefs; they may be breaking for some other reason.

Someone needs to check the config files and see that things are actually set right there -- the settings don't seem to be visible yet as the production ones are, cf bug 27154.

Changed bug summary and product/component to reflect this appears to be a prototype-specific config issue.

I just got a email for my account creation, So the email part does work.

The prototype server is being decommissioned hence any issue with it will disappear whenever the shutdown button is pressed.