1. It is harder to see if your crack was successfully completed, especially if the degradation happens late in game.
2. If the game is fun until it goes wonk and the person learns it is pirated, they may decide to buy the real deal.
3. The potential damage, if you didn't have a noticeable false-positive rate, is limited and for those unwittingly hit and find out their software is pirated, they're likely to not buy/get from the downloaded source again.
4. From the standpoint of a developer, it is creative fun.Yeah, I get that maybe it made the developer and/or publisher feel some kind of 'justice' was done, but it's ultimately bad for your brand to have any game out in the world that has subtly degraded performance. The players of pirated versions probably just assumed the company makes games that are buggy or with really bad difficulty scaling. Reducing piracy by making players not want your games doesn't seem like a winning long-term strategy.
Some publishers instead layered their piracy checks later in the game play or delayed stopping pirated play until some number of game events after detection. If they were concerned crackers would find an explicit error message, another option is to change game play in some other way like this game ended the luge race before the player finished. A legit game behavior at the wrong time is still harder to find than an error box or specific text.