150 years is along time for something to go mostly unused and retain it's usefulness.
The Samurai are gone, the fields they fought on haven't been covered in blood in a long time. The world has changed.
Heavy Cavalry where once a force to be feared... now they aren't. And even if we could go back to the technology and line up and face off before battle ways when they where, It would be a long time before the ability to effectively train and use them returned.
Down in the States people have been recreating the civil war for years, Do you think they are as effective with those weapons and tactics as the real soldiers where? Do you think they could train soldiers as well for that type of war?
If something isn't used it goes stagnant. It also was not a primary concern of a samurai, they had weapons to fight with, empty hand training would have been a secondary concern if that. More of a "If you are really really foobared already and have lost all your weapons and can't retreat, well what the heck, give this a go" priority.
That is never going to match the hand to hand skills of someone that only trained hand to hand and fought hand to hand. But why shoud it? They had swords and bows.
The it worked on a ancient battlefield is faulty logic, cause for one it's been 150 years, nothing stays the same over that much time. And If it did these where people that fought with weapons, not there hands. We also have no idea why they trained empty hand at all... It could have very likely been like much of todays military hand to hand, not as much for direct application on the field, but to train toughness, aggression and get the soldiers fighting without killing each other.