Analects (Book 7.21): “The Master said, To know when you know, and to know when you do not know — this is knowledge.”
There's a strong obsession in the West with having an answer to every challenge, with asserting oneself in all manner of challenges presented to one's faith. I'm here to argue that we should not assert this in Shinto.
Anyone familiar with Shinto understands its broad cosmological themes: core virtue ethics, very little ontological or moral guidance with the exception of common sense and a few scattered parables, a simplistic view of the afterlife viewed through the lens of the Kami, and a strong bond to your community and your actions as they directly contribute to that. This often contrasts Christian, Buddhist and Muslim views: very strong deontological ethics with legalistic rulesets, similes, parables, sayings and scenarios galore to reinterpret and use as guidance.
At first glance it may seem like we are at a clear disadvantage. That only is true when framed as a win/lose debate of wits. But let's take a step back: In the greater scheme of things, a dilemma or challenge only bothers you if you choose to let it. You can confidently look another in the eye and say "I don't know. We don't really address this." and rather than seeing it as a retreat or admission of defeat, instead see it as you humbling yourself.
"The affairs of the palace do not fill the rice bowl." as is often said in Japanese. Shinto's history as a religion of peasantry and farmers reflects the contentedness of not needing to understand every aspect of the world.
So, when an atheist asks me if I believe in evolution and if it contradicts Shinto, my first response is not to give him an answer, but to ask him, "How does knowing or not the history of evolution impact my relationship with the Kami, nature, and my community? I have no need to answer this question. I am not a scientist nor a schoolteacher. If you ask me if people should learn evolution or some variety of creation, I would say that leaving this decision up to a humble tradesman seems unwise."
Rhetorically, I don't need him to answer, I've already made my point. While he's learning about evolution, I think about what my next workday looks like, or what I'll be doing on my weekend. I live, knowing my life can be wasted answering other's questions or I can fulfill my needs and wants.
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