The answer is surprisingly simple and banal - Laurence Fishburne was simply not invited to the shooting. The actor himself was not upset, and in his commentary he explained that although he considers his role in The Matrix one of the most significant in his career, he wants the audience to remember him from other works.
It can be added that Joe Pantoliano, who played the role of the traitor Cypher, was not invited to star in The Matrix 4. However, this actor did not agree with this state of affairs, and wrote to Lana Wachowski about his desire to participate in the filming of the fourth part. However, there was no response from the director.