Mhh, no he does not have KA, but it may be that Shisui used it on Yagura for whatever reason to help Obito. Perhaps as a favor to make Obito either stay away from Konoha, or make him help in the uchiha massacre.
The other option is that Danzo needed to do Obito some sort of favor. Shisui could had been in root, which would explain a lot of things, and thus Danzo ordered him to use KA on Yagura, with the command to obey Obito, but then again, this wouldn't make sense, since Danzo should then have known about Madara, unless he actually knew that Obito didn't die, and had Obito working for him secretly for some years.