If a customer sent an apology email for his delay response to an email I sent earlier, what is the best way to reply to such email?
It depends. Some examples depending on the situation:
"That's fine, no problem at all".
"No problem at all; the item you were waiting for will probably arrive in five days time" if their delivery is delayed.
"Thanks for informing us, but we had to make a decision how to proceed without your input and decided to do X. If you don't agree then call IMMEDIATELY. "
"It's very unfortunate that you didn't send this email earlier, because without the information that we needed urgently the court case has completed and you lost, and you need to leave your home within the next seven working days or you will be thrown out by bailiffs".
This is a broad question because we have no idea of the circumstances involved.
So the answer is "It depends".
If the late response doesn't affect anything in a negative way, then just replying with "That's ok, no problem.", is fine.
If there are consequences, then you can lead with "That's ok, I understand", and then go ahead with whatever the next steps are.
Without knowing the circumstances, it's impossible to give you a clearer answer.