if you have AllowOverride on for Apache, then Apache will check for an .htaccess file in each directory. Since each Moodle installation has a number of directories, this can slow the server - or conversely speed it up if you remove diretories.
It looks like you all use an HTML splash page to point to the different Moodle installations, you can do something similar on a single installation by setting up categories and pointing the splash page links to the different categories.
However, a downside to one installation is if you need to keep your users fully separated by installation - if you move to one site then anyone who can use Assign roles will see all the users on the installation - which may or may not be an issue depending on your school's policies.