as you want you can change global settings for vhosts to accept .htaccess directives or do it per site in ispconfig system, best practice is dont allow users .htaccess if they dont need it or dont know what that is :-) that is for security reason.
Global directive can be placed in..
at the end of file
Options +Includes +FollowSymlinks -Indexes
Allow from all
<Files ~ "^\.ht">
Deny from all
For Joomla that will be enough. But that is not recomended setting...