Permissions – What is the structural difference in this case (4 document libraries versus 2 document libraries with nested folders)?

What is the difference between 4 different document libraries (AC, AD, BC and BD) and two document libraries (A and B) and, in each of them, two directories (C and D)?

It seems to me that this would be the same thing and as regards the groups / security permissions, unique permissions can be assigned to each one of them for each document library or each file.

So what is the difference between these two, and what is the recommended way and why?

Thank you so much!!