You can hide a SubPanel in an upgrade safe way but unsetting the subpanel via PHP.

Example:

You can hid the Leads SubPanel into Accounts module by customizing the custom/modules/Accounts/Ext/Layoutdefs/layoutdefs.ext.php, which is a upgrade safe customization. Add the following to the end of the file, before the closing PHP tag.

unset($layout_defs['Accounts']['subpanel_setup']['leads']);