You mean the "Harmless Red Cube" background thing? It's a reference to a beta-tester named "DeadlyRedCube", and it's just a background thing with no effect whatsoever.
Yeah, the red cube confused the hell out of me. The first time I saw one, I stood in front of it trying absolutely everything I could to make it do something. Also, dirt patches. If they do anything I still haven't figured it out.
You (used to) use them to plant spores to get mushrooms as an alternative to corpses, I believe. Spores were an item that you used to get by using the level 1 skill in Fungal Arts, but it was changed to the current on-kill proc because using the skill every time the cooldown ran out, and then individually planting the spores on corpses/dirt got extremely tedious. They're still in the game files, but I don't think there's a way to actually get them anymore.
It is not like the there weren't enough corpses, but damn it was tedious. The only tedious thing left in the game is putting your keys down and then kicking open a door and then picking your keys back up again.