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Do you get an error stating that these can not be removed, or do you deduct that information because these directories exist after running the cleanup?

In the latter case, Admin Tools did remove those cache directories, but they are created afresh by Joomla! during the next page load. This is part of the normal operation of Joomla!. The only way to have Joomla! not create them is to turn off caching in your Global Configuration, but this may have an adverse effect in your site's performance.

User with ID 99 seems to be the "nobody" user account on your system. Please note that "nobody" is a username. Unlike what you said, it doesn't mean "no owner". There is always a special user called "nobody" and a group called "nogroup". These are a user and a group which get denied any administrative privilege. It's the user and group under which most services –including Apache, your web server– run. Since you have not enabled Joomla!'s FTP feature in your site's Global Configuration, the cache files/directories are created by writing directly to them. Joomla! runs inside PHP, PHP runs inside Apache, therefore all three run under user 99 ("nobody"), ergo the ownership of the files & directories is user 99.

Kickstart works on the same way. By default, it uses direct file writes. Kickstart runs inside PHP, PHP runs inside Apache, ergo all three run under user 99. Writing directly to files causes all extracted files/directories to be owned by user 99. And that's exactly why there is the "Use FTP" extraction method. Please read the documentation for more information. While you're at it, read Akeeba Backup User's Guide "Security Information" chapter. You may have to read it a few times to let that information sink in. In fact, you ought to read that chapter. This is web server administration 101, you really need to know all of that stuff.

See? It all makes sense now.

You're welcome! I'm glad I could explain that - this topic seems to be the bain of the existence of many a web site owners :)

Regarding the .htaccess file, the easy explanation is the best. A typical .htaccess file can be produced by renaming the htaccess.txt file which ships with Joomla! to .htaccess and leaving it in your site's root. If you are interested in security, you can use Admin Tools' .htaccess Maker to create a .htaccess file which will lock down your site as much as possible. Please, please read the documentation before and while using the .htaccess Maker. Applying it will certainly break something (setting it up is a matter of trial and error) and you have to be familiar with the documentation's instructions to resolve any issues. If you follow the doc instructions it's very easy and shouldn't take more than 30 minutes.