Historically, it seems like the legality is a bit fluid, and depends on how much money someone is willing to spend to stop you. What the Pirate Bay did was legal in Sweden until the big companies applied pressure and resources to stop them. I wish we lived in a world where laws could be interpreted clearly, but at least it seems like big money can have its way regardless. So, in your hypothetical website scenario, would someone powerful be very upset, or would it not be worth it for them to go after you?

You could do unintentional linking if you don't want to be subject to DMCA claims, like putting in the description

"We do not provide support for external projects that use our code, like shadow-website. Please contact them for further assistance."

or

"If you're using external services like shadow-website, please say so while reporting issues/bugs."

This gives off an air of legitimacy to the shadow-website to anyone who's interested in looking at mothership, but doesn't explicitly associate it with mothership.

The links themselves can't really be copyrighted.