This is just a hunch, but I suspect that devices that only got the May HotPatch update excludes that folder as that would be considered a non-security/quality update.

Versus machines that got the "full" May LCU would have.

Again that's a hunch, but I suspect that's the case. My home system has the folder. My work system (which is getting Hotpatches) doesn't.

The May 2026 Windows security update for some versions of Windows introduced the folder and example scripts. This is the documentation in the KB release notes: 

• "This update adds a new SecureBoot folder under C:\Windows on eligible devices. The folder contains example scripts intended for organizations with IT professionals who actively manage updates across their device fleet. These scripts can be used to detect Secure Boot certificate update status and automate deployment via a safe rollout mechanism in an Active Directory environment. For more information, see Sample Secure Boot E2E Automation Guide."

Updates for these Windows versions included the scripts:  Windows 10, version 22H2 and version 21H2, Windows Server 2019, Windows 10 Enterprise LTSC 2019, Windows Server 2016, Windows 10 Enterprise LTSC 2016, Windows 11 version 23H2, Windows 11 version 24H2, Windows Server 2025, Windows Server 2022.

These scripts are documented at: 

Monitoring Secure Boot certificate status with Microsoft Intune remediations - Microsoft Support  

Sample Secure Boot E2E Automation Guide - Microsoft Support