A linked page is a mirror of your other page, i.e. whatever changes you do on linked page affects automatically the your page and vice versa. It is like a virtual representation of your page in a different folder of the tree of content.
If we take your example - this essentially a way to build a navigation without copy/pasting menu pages. Lets say you have top navigation menu and bottom navigation menu, and you want only some major items from the top menu to appear in the bottom menu. You create a bottom navigation folder and add there linked pages (linked to menu items in the top menu). So lets say your top menu has 20 items, but only 5 of them should appear at the bottom. You add 5 linked pages to bottom navigation menu folder. Your bottom menu repeater should display everything from this bottom menu folder.
So yes the only way to remove from the bottom menu is to delete the linked page, but that is OK. You don't delete the actual menu item you delete it is virtual representation of it.
p.s. Technically you can create Boolean properties for your menu item page type, i.e show in the top navigation and show in the bottom navigation, so each your menu item has 2 extra check boxes.
But you just need to understand how to use linked pages and you'll be ok.