Indeed, when a project is created, there is no "lib/kendo-ui" folder. This is because, by default, the project uses our CDN and has no local Kendo files.
To add the custom theme, you can create such a folder and register it in the "~/Views/Shared/_Layout.cshtml" file. More information about this is available here - https://docs.telerik.com/aspnet-core/getting-started/installation/getting-started-copy-client-resources. Once you include the custom theme, remove all other Kendo related styles from the "_Layout.cshtml" file.
I hope this helps.