If you are using the native integration direct to Prism Element, when you check the UEFI it will set both the UEFI and Secure boot on the Nutanix side. The issue is that Nutanix requires the machine type to be changed to Q35 which we are not sending. I believe this just got fixed internally and should get pushed to a release soon. A work around would be to create your Windows image using legacy boot until the fix is out.
If using the Prism Central plugin then with Windows it is not tagging the payload as sysprep so it will deploy as uefi and secure boot but wont currently customize. Like Chris stated above this plugin is being worked on and should have this added soon.