I could be wrong, but my guess to the reason Yamaha (and other manufacturers) only have one of the 2 headlights hooked up is likely a power consumption issue. The Alternators in these sport style bikes are not as large as in cars (or big touring bikes), and they have a very hard time keeping up with the power demand and also keeping the battery charged. I know one of the potential problems with the FZ with any additional electrical components is the battery running down if the RPMs are not consistently above a certain point, such as when you are in slow moving traffic jams. This becomes a real problem when you have extra electrical components hooked up. The headlights might be the largest single power consumer, so 2 of them starts to stretch the capacity a bit. Since you don't use your brights very often, and you would probably only be using them when you were moving and had the RPMs up, they don't really create a big problem. But having an extra headlight on all the time adds another large power consumer to the mix. The motorcycle manufacturers know what the basic demand of all the electrical components are, and they are not going to set themselves up for having more demand from stock components then the basic setup will allow. If they manufacture a bike that has problems keeping a battery charged, they would have many headaches. It would be nice if they put a larger alternator on, but that would drive up the price and add extra size to something.
Motogiro and some of the other electrical gurus might have a better explanation as to why only one headlight is being used in the stock configuration on a lot of these bikes. I don't think it has anything to do with the manufacturers being lazy or trying to save a couple bucks (or cents) with only one headlight. It would literally only add one wire at most to their configuration. They already have everything in place. It's a common configuration with a lot of motorcycles that have 2 headlights, and only one is on for the low beam. I think it's purely a consumption issue.
With all this said, I have done BD43's dual headlight mod on my FZ, because it looks goofy as hell to only have one light on. It's even more of an eyesore with lights that are shaped like they are on the FZ. If it was 2 round bulbs closer together like a Triumph triple speed, it might not look as goofy.
But, I'm also very aware of the power consumption issue, and I'm religious about hooking up a battery tender every time I finish riding, to make sure the battery is at it's best when I am ready to ride. If I forget to hook up the battery tender, I notice a difference the very next time I go to start it.
I also added a waterproof push in splice connector (pic attached-red connector) to the wire used for the headlight mod. If you ever have to completely remove the front cowling that houses the headlights, you have to be able to disconnect that wire, and now I also have the ability to disconnect the dual headlight mod very quickly if I needed to save some battery in an emergency. I put the disconnect location at the same point as the 2 other larger disconnects for the wiring harness on that cowling.
Obviously, if you hook up any other extra power consumption items, that adds to the already overtaxed electrical system. Make sure you keep this in mind when doing additional mods.