Soybean is cleistogamous, meaning it is highly self-pollinated. However, you can easily hybridise soybean by emasculating flowers and artificially pollinating. Your statement that cleistogamous flowers produce better pod set in artificial pollination is not clear. Cleistogamous flowers, on the other hand, produce better pod set when there is no bee activity or other factors that prevent cross-pollination.
Hand pollination may be a good tool for getting better size of pods but the percentage of better size pods will be low as predicting the susceptibility of stigma is bit difficult. honey bees and some other bees those helps in cross pollination can be controlled by some trap crops