The main difference between the regular wire core brushes and the softdub version is that the softdub brushes are constructed with thread. This thread is twisted tightly together, trapping all the dubbing material in place. They are slightly better suited for smaller patterns and dry flies.
I use both styles on all my nymph patterns and do not see any difference with the tying process or in the finished fly. Give them both a try and I'm sure you will be happy with the results.