His numbers against fastballs over 94mph are poor, yes. It's also important to note that he hasn't faced many fastballs over 94mph, either, so the sample size and his practice against them are limited at best. NPB just doesn't have many velocity-throwers.
It's also not an impossible fix. Michael Busch was someone who struggled against velocity and he had a .314 wOBA on fastballs over 95+mph last year which, while it isn't elite, is more than enough.
We know lots of the metrics on Murakami, when he hits the ball, are elite. How much of this is mechanically induced versus anything is hard for me to speak on. You'd assume, if the Cubs were the team that spent $90m on him, that they believe it's a fixable thing. While I know that's an "appeal to authority" argument, I think there are teams you can appeal to (and I think the Cubs more or less fit into this territory) and teams you wouldn't (the Angels or the Nationals, as an example).