> What reasons are there to decline a visa to a PhD employed in a critical industry?

Protectionism of course. The fear is that companies are looking for cheaper foreign labor. Ironically, when allowing some visas with many strings you end up with indentured servants that push labor prices down, not up.

A train of thought is that there's no such thing as a labor shortage, only employers unwilling to pay for labor. Of course it's all very complicated. Attracting top talent is also good.

It's not easy to know what the perfect policy is but there are lots of arguments to sort through.