While processing-wise you probably don't need two or more Megas I prefer a networked model closer to your second picture. It is more complex because you need a protocol to talk between nodes but it distributes the processing and if one box fails the others carry on (or they should if the system is design well).
Personally I've never liked the central master with a 1000 wires running around the house but software-wise it's a simpler model and a lot of people prefer it.
Do you plan to have momentary push buttons to control lights etc? If so where's the redundancy? How do you turn a light on when the Mega shits itself or you upload a new program version and it has a bug that takes 3 days to fix?
Rob