This is an extremely interesting question. For a game like Minecraft, I definitely believe it's at least broken even because the game has quite a long lifespan and has viral aspects in that people enjoy sharing what they create in and with the game. More users means more talking about the game, which means more sales.

For other games, I think piracy can definitely negatively affect the total number of units sold. This is especially true for hollywood style big story heavy big productions that are only expected to sell well and stay in the public conscience for a few months. That still doesn't mean anyone has actually LOST any money, as a bad review also can affect the total number of sales, and hopefully nobody thinks it would be sane to sue magazines for "loss of profit" over bad reviews.

And for a few games where there's a per-user cost, piracy can definitely be directly harmful to the company.