It's not possible to hide the System Designer option with basic system tools.
Still, you may simply limit the access rights for this role or not grant any administrative rights or access for this role, this way even though the user sees the System Designer they won't able to apply any changes to it or open the corresponding System Designer sections.
More detailed information about access rights and system operation permissions can be found in corresponding articles on our Academy.
For CSS that I want globally available in the application I use MainHeaderSchema.
Oleg's solution is great too, however does require overriding the BootstrapModulesV2 which can cause issues if there are other things that are needed to be loaded there from ootb modules. The CSS approach is a bit "hacky" but gets the job done easily.