I've heard it said (here in this forum) that you should only let a few shoots go up each string, and prune the rest. This supposedly improves the vigor of the shoots.
I heard a guy on NPR (he was talking about trees) who didn't agree with this idea. He said that if the "weak sister" shoots, or branches, had leaves and were healthy, then they were at least pulling their weight, and not detracting from the plant. He said you can prune for shape if you want, but cutting off healthy parts does not improve the overall vigor of the plant.
I've been wondering about this myself. There are many factors to think about here.
First off why did people start doing this: well is sure make things easier if your growing hundreds of plants. But what if you have five or six... So for agriculture it works, but is it best for horticulture?
From the botany side of things; Cutting a plant will cause shock, which will slow it's growth down for up to a week. Hops are quite strong plants and are less effected by this compared to many other plants. And on the flip side; a plant that undergoes traumatic stress may produce flowers/fruit sooner and more prolifically, as an "oh s***! I'm going to die! make babies!" response.
Another thing to consider is plant hormones. I'm not an expert on this, but the plant produces hormones which cause the plant to grow and flower. Some of these are simply less dense than other fluids in the vascular system and thereby "float" to the highest points of the plant. By removing parts of the plant, your taking these away from the plant.
Sun light is something to consider too. In an agricultural setting the 2 strings work well, but when you have just a few plants, and a lot of space, you can train them to get more light. Last year I set up netting at about 45der. This gave a large space for the plant to grow on and a lot of light for it to grab. I kept it branchy rather than just a few bines. It was a first year plant, and I had no control, so I have nothing to compare it too. But I did notice something which brings me to my next point.
Only the stronger bines produce flowers. Last year I had a lot of spindly bines that did nothing. The only ones that made cones where the thicker, stronger ones. So if you let a rhizome put off 20 shoots, the energy that is stored and what the roots can take up will be divided by 20. This will result in smaller shoots. This may mean more plant matter (leaves and stems) but no flowers. I think this is the most important thing to think about/study to determent the ideal garden growing of hops.
Pathogens have been brought up, which is a good thing to think about. It would seem that the traditional string method would reduce the potential for problems. I don't have any data on this, and doubt that it exists.
So in conclusion; I think some testing needs to be done here. The standard system of growing hops seems to be based on agricultural systems which don't necessarily apply to the hobbyist. The act of removing parts of a plant defiantly effect it in some way. The way in which the plant is structured will effect the sun light it gets, and potential for mildew. This year I am growing 10 plants in a more traditional way, but would be trying other things if I had more space.