The NewYork Post says this is the real reason
“They ‘shunned Kanye West and Kim Kardashian’s wedding because it was too low-rent for the Jay Z/Beyoncé brand’. They are guarding like hell their status. Beyoncé wasn’t going to allow a Kardashian to socially climb her. And Jay didn’t want Kanye with Kim – he thinks it’s bad for business. I think Jay lost a little respect for Kanye there”