Not sure if I word it right.Is it stronger to have 12 strans divided 3 ways over 12 strans divided 2 ways?
I think equal bundle tension is the key, I usually just make two bundle strings since I have only two colors of material and havent figured a good way to keep track of whats what when twisting a 3 bundle. I don't notice much difference in the feel of a 2 vs. 3 if properly made. 12 strands is still 12 strands just make sure they have equal tension and you should be good.
For continuous filiment fibers (such as you have in B-50 or any of the modern fibers)you don't get any increase in srength by plying. What is important (as RightTrailWrongTime said) is that you have equal bundle tension. If one or two strands are tighter then the average, or if one bundle is tighter than the other then you would have unequal stress allowing for easier breakage. The low stretch fibers in fast flight would theoretically be more sensitive to this.
Twisting, plying, and cableing do have a major effect on short staple fibers such as cotton, wool, spun polyester, and flax. Too little twist will allow slippage of the fibers resulting in low break levels, and too much twist can cause a yarn to break at lower levels. Plying does play a major role with these short length fibers as it averages out the unevenness of the strands as well as reducing the liveliness of the yarn.
Overbo, I didn't mean to get carried away. Some will say that 3 bundles will give you a more rounded string, but two look pretty good. it won't be any stronger. It does give you an opportunity to use three colors in an even barber pole twist. Personally I don't think it's worth the extra effort.