As Joomla and Moodle are different platforms the templates / themes of each do not impact the other. Therefore, you can choose any Joomla template you wish. That said there may be some issues related to the space required for your Moodle content and what your Joomla template provides. Eg. If you are using Moodle in a wrapper and you install Joomla modules down the left and right side then you may have width issues. Therefore, you will always need to plan the site design just like any other website installation.
For the Moodle theme most people will choose a navigation less theme, there are a few free ones in the download section here, thus removing course navigation from Moodle and using the Joomla Menus instead. This will give a seamless appearance to your students / users.
