The root of the problem is why customers respond well to these videos: they're surprised and impressed that the CEO of the company would take time out of his day to record a thank you video just for them. And the fact is: the CEO did not. It's deception, plain and simple. Not big, evil, Theranos-level deception, but deception still.
To put it another way, how do you think customers would respond if, along with each email, you included some text saying "this video was automatically generated"? I'd assume pretty poorly. The difference between that response and the actual response is the value of the deception here. I think that "if we were honest about this, customers wouldn't like it" is a good litmus test for whether you're doing an ethical thing or not.
Really, I think this is doing a sort of trust arbitrage. The tech exists to fake personal videos now, but customers aren't widely aware of it. You can take advantage of that difference with stunts like this. In a few years, people will know this can easily be done and the value of personal videos will drop. At some point it'll be no different to the average customer than an email with "Hi <name here>!" or a letter with faux-handwriting on it.