It has to do with anticipated current draw.
Typically, the cords can only handle maybe 10 amps safely, even if rated above that. At least, figuring from a safety margin standpoint. You can push it above that.
If you anticipate 10-12 amps per bank then I'd use two separate circuits for them, unless you know what else is on that circuit. Most circuits are rated for 20 amps, some less than that (check your circuit breaker for actual ratings.)
If you're under 20 amps total (or whatever the circuit breaker is rated for, minus any other load on the circuit) you can plug both cords into the same outlet.
If you're under 15 amps total, wire it for one cord.
16 strings of 100 minis would be about .4 amps each, or about 6.4 amps if on at full brightness simultaneously. I have a 32 string megatree on a 16 channel controller that has a single cord; that would be 12.8 amps realistically. I figure 15 amps for safety margin, which leaves me 5 amps for other uses on that circuit.