It is definitely bad practice to try to move themes (or uploads or plugins) outside of the wp-content folder. WP’s structure ensures that WP can find all the necessary resources. Anytime you move things outside of its structure, odd quirks and broken bits tend to appear. So, stick with /wp-content/themes/your-theme-slug/ and make things more dynamic.
I would suggest that instead of hard-coding the links, you use wp_nav_menu() instead. You’ll set up a custom menu in your theme one time. From then on, you edit the links within the menu inside wp-admin – you can either use the Customizer or the Appearance > Menus page.
functions.php file in theme:
<?php // add theme support for menus
add_action('after_setup_theme', 'wpse_add_menu_support');
function wpse_add_menu_support() {
add_theme_support('menus');
}
// add a particular menu
add_action('init', 'wpse_nav_menu');
function wpse_nav_menu() {
register_nav_menu('topnav', 'Main navigation of the website');
} ?>
header.php file in theme:
<?php // display the menu
wp_nav_menu(array('theme_location' => 'topnav', 'container' => ''));
?>
Then manage the links in a WYSIWYG way. Another benefit of doing things this way instead of hard-coding is if you ever change the permalinks of any of your pages, WP will automatically update your navigation, because it saves the ID of the post rather than the slug/permalink.