I found a solution to my initial problem of creating categories in bulk, however I don't mark the question as closed, if you know a better solution - please post.
MediaWiki has an import functionality. With your admin account go to
http://yourMediaWiki/index.php/Special:Import
This allows you to choose to import an xml file, which has to follow a certain structure: see here
For a category with the name "Test Category" and the text "Category Testing", you have to create a 'page' element like this:
<page>
<title>Category:Test Category</title> <!-- Name of the category, don't forget to prefix with 'Categroy:' -->
<ns>14</ns> <!-- 14 is the namespace of categories -->
<id>n</id> <!-- identifier for category -->
<revision>
<id>16</id> <!-- number of revision -->
<timestamp>2013-02-10T22:07:46Z</timestamp> <!-- Creation date & time -->
<contributor>
<username>admin</username> <!-- Name of user who created the category -->
<id>1</id> <!-- ID of the user -->
</contributor>
<comment></comment> <!-- Comment about the category. Can be left blank -->
<sha1></sha1> <!-- sha1 hash can be left blank -->
<text xml:space="preserve" bytes="1">Category Testing</text> <!-- It seems it doesn't matter what you write into the bytes attribute. -->
</revision>
</page>
If you want to create hierarchies of categories just add the parent category tags into the text element. Say the category should be part of the 'Parent Category' category then the text element should look like this:
<text xml:space="preserve" bytes="1">Category Testing [[Category:Parent Category]]</text>