Bug 27031: Use Koha.Preference() more often in header.inc and js_includes.inc

Bug 27031: Use Koha.Preference() more often in header.inc and js_includes.inc

This patch uses the Koha.Preference() macro more often in key includes.
(In the longer term, it will help reduce dependency in problematic C4::Auth code.)

Test plan:
0. Apply patch
1. Go to http://localhost:8081/cgi-bin/koha/mainpage.pl
2. Note "Cart" link in nav bar
3. Click "Cart" and note "Your cart is currently empty" text
4. Click "More" and note "Course Reserves" in dropdown menu
5. Go to http://localhost:8081/cgi-bin/koha/catalogue/search.pl?q=test
6. Click "Select all" above search results
7. Click "Add to cart"
8. Note "Cart" now has 3 displaying next to it
9. Click "Cart"
10. Note there are three titles in the cart
11. Click "Empty and close" and click "OK" to confirm
12. Note "Cart (0)" now appears in the top nav
13. Go to http://localhost:8081/cgi-bin/koha/admin/preferences.pl?op=search&searchfield=IntranetNav
14. Save the following content in the system preference: <li><a href="/index.html">New Home</a></li>
15. Refresh the page
16. Note "New Home" appears in the top nav between "Cart" and "More"

Signed-off-by: Lucas Gass <lucas@bywatersolutions.com>
Signed-off-by: Katrin Fischer <katrin.fischer.83@web.de>
Signed-off-by: Jonathan Druart <jonathan.druart@bugs.koha-community.org>