Q1: How to delete submenu items?
A1: Edit xoops_version.php
It's just a fib
xoops_version.php MUST be modified with updated modules.
Who can hack xoops_version.php, again and again?
First, you should finish using "Main Menu" from system module if you want to control menu items.
You should learn "Main Menu" is one of the most heavy blocks because it crawls all xoops_version.php under active modules.