is there any effect on Pin change interrupt in pin13 because of built-in LED ?
Not on the pin change interrupt part of things. But depending on the board (older Uno's and Nano's /. Pro Mini's), pin 13 might be a bit harder to drive.
pin 13 might be a bit harder to drive.
So it is better not to use it then
Like I said, depends on the board.
But besides that, I always try to do something useful with the free onboard led. So if it's useful to also see the led lit I would go with it. But it does depend on what drives it and which board if it's electrically possible.