KAGA was damaged in the Palaus much earlier but had operated nonetheless as an integral part of KdB in the Darwin Raid & the Java interdiction ops. So, she was overdue for repairs in a Japanese port. I am not aware that her absence in "C" Sakusen seemed to cause any significant problems in that mission. (?)
However, and very interestingly, Senshi Sosho Vol. 26 states that KAGA was to be detached from Cardiv 1 and operate independently as part of the South Seas Unit from April 10 in the Second Stage Phase One ops (to last until ~ late May), but her lengthy time in the yard altered those plans....
Those included the Port Moresby operation after the IO raid, but her repairs took so long that CarDiv 5 was utilized instead. (The thought was also that the two junior carriers needed more ops as training, too.)
BTW, the Japanese system of having their carrier air units operating as part of the ship's organization was known as ku-chi ittai (meaning, roughly, 'air & ground as one body').