A namespace, as you say, is a directory. You can create a page by accessing it from your url. If you prepend a namespace, and if the directory does not exist, the namespace together with the page will automatically be created once the page is saved:
http://my_domain/my_wiki/doku_php?id=new_namespace:new_page.
This will open
new_page[/m] in [m]new_namespace. You can also do this by creating a link in one of your other pages to the non-existent page, and when you click on it, the new page will be called up. When you delete the content from the page, it is removed from the file system. However, its metadata and history remain, so another page with the same name will inherit those.
How you organize is up to you. Namespaces can have sub-namespaces, just like directories. A page can belong only to one namespace.
There is a tag plugin, so that more than one page can be tagged with the same tag. Clicking on a tag opens a list of all pages with that tag (see:
https://www.mturner.org/fckgLite/doku.php). As for navigating, that can be done with the sitemap and/or a sidebar holding a navigation plugin, like indexmenu. The link tool has a search box which will find all pages with a given name whatever the namespace.
You can change the name of the start page in the Configuration Manager. You can't make links absolute in the sense that your mean. and I can't talk about the g-fonts plugin, never looked at it.