Hello
According to our documentation, if you have Windows 11 E3 Licence, then this gives you the benefits of Windows 11 pro as well as per user licences for Azure Virtual Desktop and Windows 365 instances. https://www.microsoft.com/en-us/microsoft-365/windows/windows-11-enterprise. You do not need a M365 licence if you do not need those services.
I will highlight that the M365 E3 and E5 suite comes with various security and productivity features. I would review the feature lists here to find out which licence best suits your requirements. https://go.microsoft.com/fwlink/?linkid=2139145
kind regards
Alistair