This is Max from the Shopify Team.
This can happen depending on the settings of the customers' email. Sometimes, automated messages like notifications are filtered into spam or junk folders. One option I'd suggest to help with the potential customer confusion is to display a message on the cart, or the order status page encouraging customers to add your shop email to their contacts list (to avoid the spam folder).
For repeat customers, asking them add your email address to their contacts list will prevent further communications from going to spam.
You could also add this information to any FAQs or contact pages, to be thorough! It looks like you have a Help page at the moment, but, I'd suggest looking into these blog posts for some advice on different pages and why they're useful;
If you have any more questions, please let us know! I hope this added info helps.