For the deduplicated styles, do we really need the <link> tags? Couldn't we completely remove the tag?
It doesn’t do anything bad to keep them, the only thing that might be interested in removing them is probably mobile version (since every byte seems to count there).
I don't see any particular reason to do this specifically in MobileFrontend. More generally, this is a matter of distinguishing between canonical HTML and presentation mode.
When editing in VisualEditor, or when rendering partials of pages on mobile web or mobile apps, it is important that the client can keep the stylesheet around, even if it removed the section it was a part of, as long as there is another section that had a reference to it. Likewise, when a section if viewed without any references to that template, it can be omitted.
However, for page views as output by a skin (Vector, Minerva, MobileFrontend), they are indeed not needed. It seems like this falls in the same category as a lot of Parsoid attributes not needed that we strip on rendering. Except this is the first (obvious) instance of such concept for the PHP parser output.