Hi,
I believe there is no simple configuration that hides these 3 nav. items, they are part of UCI Application Design.
However, you can change the Navigation Type of your app from Single Session to Multi-session.
You can update your App's customization.xml, to change <NavigationType> value (from 0 to 1):
1
If you change it to 1 (Multi-session), the type of interface is changed and No Navigation Item is shown (including Home, Recent and Pinned):

You can open the New Tabs by clicking on ' ' icon.
I am not sure if this is an ideal solution for you or not, but it hides all nav. items including Home, Recent and Pinned.
Here are the steps to update the Navigation Type:
- Go to Advanced Settings -> Customization -> Solutions.
- Create a new solution and add your existing app.

- Export the solution (unmanaged) and extract the zip file.
- Open the customizations.xml file in your favorite editor.
- Look for <NavigationType> under <AppModule> and change the value from 0 to 1.

- Zip the files and import the solution back in CRM.
- Publish All Customizations and refresh.
Here is the link to Microsoft Docs on this property:
https://docs.microsoft.com/en-us/dynamics365/customerengagement/on-premises/developer/entities/appmodule#BKMK_NavigationType
You can see detailed steps in my blogpost here:
https://community.dynamics.com/365/sales/b/crmlogs/posts/dynamics-365-ce-switch-uci-app-from-single-to-multi-session-navigation
Let me know if you need further clarification.
Best,
Wahaj
(if it helps, please mark it as verified)