This should have the same behavior as core for all namespaces.
Reported at WP:VPT on enwiki.
See https://en.wikipedia.org/wiki/Special:WhatLinksHere/Special:Preferences for an example. MediaWiki core does not include links to Special: pages in WhatLinksHere. Flow, however, does include these links in link tables.
This is confusing and should not happen, not least because the WhatLinksHere form does not list Special: in the namespace dropdown.