It appears that Horie Yui really has left her long-time agency, Arts Vision. There has been no official announcement, but her name is no longer on the list of seiyuus on the Arts Vision site.
Following the arrest of the president of the company for sexual assault of a teenaged aspiring seiyuu, the company's website shut down. The site showed only an apology and the news that the old president had resigned and a new one had been named to come in and make sure such things didn't happen again. When the site came back up recently, Hocchan's name was not there.
There were salacious rumors all over 2channel, of course, and Hocchan herself posted thanking her fans for their concern, and her agency for its support over the years, and implying that such things had never happened to her. But the editor of Seiyuu Grand Prix magazine has said that she has left Arts Vision and become independent. The absence of her name on the list seems to confirm that.
It remains to be seen if a change of management will make any change in the kinds of roles and concerts we see Hocchan doing. My sense is that she is a fairly strong force herself, and was probably already guiding her own career.
Sanpei Yuuko and Morinaga Rika have also left Arts Vision's sister agency, I"m Enterprise, to become independent.