From a historical perspective I did a bit of research for you. The Theban alphabet first turns up in 1518 (during the reign of Henry VIII) and was referred to as the Honorian Alphabet after Honorius of Thebes a Magus from the Middle Ages. Some sources do claim it was used as a substitution for the runic alphabet but I can't find anything conclusive on this and to be honest I doubt it.
I think there is a value to the Theban script as quite often a spell does involve having elements written down and it makes sense to have those in a format that isn't accessible to most people. I'm not sure there is much value to the alphabet beyond that, certainly there is no magic or mysticism inherent in it. However it does provide a link to the past and it is possible that another purpose of the Theban script is to link the witch of the modern day to the traditions of her ancestors.