So I'm trying to modify the layout of theme.yml in a PrestaShop theme. I comment out the following:
# - ps_linklist
# - ps_customeraccountlinks
The theme.yml is only useful when first installing a theme, any changes you make to it will not do anything after the theme has been installed.
However it is easy to either remove the unwanted modules on the "installed modules" page (click the little arrow next to the module and select "uninstall") or unhook the module from the, in your case, "displayFooter" hook on the "Positions" page which is found in the submenu of "Design" in Prestashop 1.7.x