Enabling subpages with $wgNamespacesWithSubpages means two things:
a) a navigational subtitle appears on pages titled A/B where page A exists;
b) relative .. and / work in links and transclusion.
Other "features" of / like #titleparts and "linguistic" meaning are not affected.

https://www.mediawiki.org/wiki/Manual:$wgNamespacesWithSubpages
https://www.mediawiki.org/wiki/Help:Subpages
https://meta.wikimedia.org/wiki/Help:Link#Subpage_feature

Filing this bug for the untracked proposal by MZMcBride in http://lists.wikimedia.org/pipermail/wikitech-l/2014-June/077267.html (see for details):

The more I look at this, the more I wonder why not instead invert the
array:

$wgNamespacesWithoutSubpages = [
    NS_FILE => true,
    NS_CATEGORY => true
];

There is also an outstanding question by Tyler in https://gerrit.wikimedia.org/r/140765 which is best addressed here:

What wikis are using this [slashes in titles] on namespaces that do not have
sub-pages *and* would cause problems if sub-pages were enabled?