There are rumors that Prince William is having an affair with her. He's into some kinky stuff that Kate was not willing to entertain, but she is.
but I think it’s Kates health
There are also rumors that Kate had bowel surgery due to a severe eating disorder and is using a colostomy bag, which she is embarrassed about. This is why she is not appearing in public.
I assume she had a hysterectomy for some type of reproductive cancer. She remained in the hospital for so long to start chemo, radiation, etc., rather than taking daily trips back to the hospital. Time will tell.