This may not make much sense to someone that doesn't actually practice a koryu art, but historical preservation of techniques is not the base idea behind them, and secrecy is a good part of why they are still in existence. The koryu began originally as family or clan traditions. These were kept very secret because everyone else was the enemy, and you didn't want the enemy to understand the basis of what you were doing. The koryu also began as political entities, with their own ideas and ways of doing things. These were mostly kept secret also as a way of distinguishing those that were in the know. A lot of this flavor is still preserved in the koryu. Not so much in the larger and more public koryu such as MJER or MSR iaido, but in the smaller, more traditional arts. Secrecy is simply a large part of the teachings, and the inner workings are never passed out to anyone that the head of the school thinks will not have the best interests of the ryu at heart.
Preservation of the ryu itself as a distinct entity is paramount, not necessarily any particular technique or form. Properly preserving the ryu for another 400 years means that the inner workings of the ryu need to be kept secret. This is because putting the inner knowledge out in the public domain would overly dilute that knowledge with myriad little changes, and you'd end up with many, many branches of the ryu that bear only a superficial resemblance to the original. While this would be perfectly fine with both MA historians, and the martial artists that would like to learn more about a particular art, it would mean the end of the ryu as it has been pased down for hundreds of years, and that is what we are charged with preserving.
Yeah, I get where the secrecy originally came from and the current motivation. I have my doubts that keeping secrets will actually increase the likelihood of the ryu's teachings surviving unchanged through the centuries. With the secrecy-based system, any changes, distortions, misunderstandings or omissions of the curriculum that occur from one generation to the next are invisible and will never be corrected. If koryu practitioners operated more like professional historians, they could compare the teachings of branch A of a ryu to Branch B or compare oral traditions to written documentation and probably come closer to estimating the original teachings. That's just my guess, though.