Did the 64GB iPhone SE ever ship with iOS 10 installed?
According to EveryMac.com/EveryiPhone.com, the 64GB SE was sold (in the US because you didn't specify a different country) with iOS 9.3 preinstalled.

iOS 10 came out in September, 2016 and I believe all iPhones after that date came with 10 preinstalled, including the 64GB model.  I can shop the Best Buy near me and they've advertised a 64GB SE with iOS 10 preinstalled.  You'd need to ensure the one you're looking to purchase was distributed prior to September.

As a standard disclaimer, I would not recommend you stay with iOS 9.  Many security enhancements were issued, and continue to be issued, with the latest versions.  You leave yourself wide-open to being compromised with an older OS.