Recently, new water repellants using chemicals called Silanes and Siloxanes, have come on the market. These chemicals absorb more deeply into the masonry and chemically bond to the masonry in a more long lasting way. These materials are considered breathable in the sense that they allow a percentage of the water vapor in air to pass through.
However, there are some problems with modern water repellant materials. The first problem is that even the best water repellants need to be reapplied by a skilled and experienced company about once every 10 years. I have yet to work on a building whose owner has shown me a log of all the things that have happened to the building before they owned it. Even a good steward of a historic building can not guarantee the good sense of those who come after them. The second problem is that it is imperative that the masonry wall will not have any mortar or masonry cracks. Even a recently repointed masonry wall can develop problems without the knowledge of the owner.
I am not a purist preservationist, I do realize the need for modern technologies under certain circumstances. I would recommend using these products under limited circumstances such as on horizontal masonry surfaces where copper or aluminum caps or flashing are aesthetically unappealing. But generally, mechanical solutions like flashing last for a 100 years or more, they are both visible and inspect-able and can be replaced by anyone.