Where it's not rare is medicine. You regularly hear the term spat out like a weapon, particularly in big hospitals.
It's a very poor way to justify something. It's a statement of the obvious: everyone agrees you should use the best or most efficient way of doing something. What people don't agree on is what that is. So it's "we all agree we should be doing it the best way, and I say the best way is ...". You get no indication of why it's best practice, or how it's been chosen, or who chose it. Its more an appeal to authority.
There is another term in medicine that's also bandied about frequently: "evidence based medicine". Unlike "best practice", it assums the obvious: everyone agrees we should be using the best way. It's telling you how the best way way chosen: from the evidence. More importantly it's also giving you permission to improve on it: find your own evidence. If you asked for to see evidence for "best practice", it's often seen as an attempt to undermine authority. If you asked to see the evidence behind evidence based medicine, the reaction your likely to see is "oh, you get it, here is what I have".
When I hear "because it's best practice" or "this is best practice" now, I shudder. It's not an invitation to be part of a team working to produce the best outcome. It's telling you you're a minion, and you'd better follow the rules.
But I think you are right in one sense, the reason we see it used far less in software development is we can often shoot something down with a few sentences of tightly reasoned logic. Evidence is often easy to come by. Medicine doesn't have that luxury, the body is too complex to reason about. It does have rigor and scientific analysis, but it takes a big studies and a lot of effort to gather.