He does, most of the time. Since Pep arrived -
Aguero has scored 11/15 (73%)
Yaya has scored 3/3
Jesus has scored 1/3
Sterling has scored 1/1
Gundogan has scored 1/1
De Bruyne has scored 0/1
So Aguero does take most of them, but his record is below the worldwide average of 75%, and the Premier League record of 83%. Not great, especially as a team competing for the biggest trophies in the game should be above average.
There's a reason Yaya took them ahead of Sergio when he was starting, and if Jorginho's playing and has a 90% success rate, he'll probably get the nod sooner or later. Someone as big on the details as Pep isn't going to miss that.
To be honest, it's not ideal having either Jorginho or Aguero as the penalty taker because ideally it'd be someone who is playing almost every game, and you'd expect both of them to be rotating a lot. Unfortunately KDB doesn't seem to fancy them.