Ok - you asked ...
There are a few reasons - firstly, with a 2-compartment setup I often found that if one queen gets herself mated before the other, or is perceived by the bees as being a better queen, then bees from the other compartment will re-locate (abscond) and join her. From a survival point-of-view, that may well be desirable, but then I ended-up with only the one nuc. I've heard others report this, so I'm not alone - but then again many others don't experience this problem ...
Ok - if you're
raising queens in divided boxes, then there isn't a problem when it comes to pulling the queen, as the colony stays behind and so continues to use the same entrance location. But if you want to remove the colony itself (say, to xfer it into a bigger box), then this can be a tad awkward - for two reasons. With a single box, you can just pull the frames, then invert the nuc box over the bigger box and give it a thump to dislodge most of the residual bees. There will always be a dozen or so which hang on and stay behind. No problem - just leave the box close to the new hive, and they'll eventually join the rest.
But - with a divided box, you can't do this - that is, give just one half of the box a thump, and you really need to leave the box on it's stand anyway so that the foragers from the occupied half can continue working.
Also - with a divided box the entrances are (say) located 9 inches from each other. When the time comes to transfer the colonies into bigger boxes, the new entrances will be (say) 18 inches apart, or more - depending on what boxes you use. Now in time the bees will adjust to these new positions, so it's not a HUGE problem - but - why make life awkward for them ? Perhaps more importantly, you now have (say) two full-sized boxes butted-up hard against each other so that the foragers can continue to use the geographical entrance locations they've become used to, when the entrances should ideally now be several feet apart. Ok, so you can then move them apart ... but again, it's an inconvenience which could be avoided by using single nuc boxes in the first place.
With a single-nuc set-up, the location of the colony need never change, and so the foragers need never make any geographical adjustment. And - if you're going from mating-nuc to full-sized box, then by the use of dummy frames in a 5-frame box, there's only ever the need for one box-swap, and that takes place at exactly the same location in the apiary. Less confusion for the bees, less work and less effort for the beekeeper.
A word about frame numbers. You mention a 2-frame nuc - that provides one working gallery between two combs. That may well be large enough if you keep your eye on progress - but 3-frames gives two working galleries: that's twice as much space, with far less chance of losing a nuc if you should accidently take your eye off the ball. It'll require a few more bees, sure, but I personally think it's a wiser size to adopt.
I'm sure others will have had different experiences and thus hold different views to my own - that's what makes beekeeping so much fun (and so confusing ...).
LJ
