If you take the capital investment needed to continue funding the 200% growth of centralized payment systems in comparison with the cost of scaling solutions like the Lightning Network, then Apple pay will soon run into problems.
I doubt that Apple pay can't handle the problem if they manage to run into. Apple is one of the biggest company in the world and No.1 in Forbes rankings and with the brand value of 182.8B dollars. I'm sure that whatever problem that they might face in the future regarding its transaction they can find a solution to that.
Obviously they can because they are sitting on world's largest privately held cash reserve. They can handle any internal situation they run into. However, that doesn't mean others won't be able to design a solution!
Slow transaction speed and high fees during higher volume is indeed a problem that LN and only LN is trying to solve! Every system initially runs into challenges and slowly they bridge those gaps. LN also has flaws which the dev team is trying to bridge! That's the reason LN has been delayed several times!
Apple pay should not be the target, rather it should just be a milestone which we will cross eventually! The success of Apple didn't come overnight so we have to be patient!