I have the Encounters expansion installed.
There is a huge colored and visually jarring note on the main menu telling me I have it installed.
Selecting it opens the browser with GOG's page for it, confirming that I indeed have it purchased.
So why again am I subjected to this very annoying ad, and what does it take to remove it?

I wouldn't mind it so much if the link would go away after installing the expansion, but that doesn't seem to be the case. Maybe they could fix this in the next Expansion pack they release.