I'm honestly not sure why they become "un-deletable". It's often a simple case of changing permissions on the folder or changing settings on your ftp client to show all files (so you can delete the hidden .htaccess). In general, there is no setting or software I can install to make people see the hidden .htaccess their scripts create. It's all a setting in the users ftp client software.

Hmm.. Strange.. I'm still not sure if there is a server setting that exists that would make an impact on this issue. I'll look into it later this week.