- People add an index.html placeholder page in their site so the actual site is not visible while they're developing it.
- People add something like
Logobecause they work on a development (aka local) server so they cannot add the actual domain - People just use the /index.php link cause this is probably what they read in some Joomla tutorial.
In reality, this is bad SEO-wise for your site. You see, Google assumes domain.com/ and domain.com/index.php are 2 different pages. So without knowing, you easily screw up your site's SEO potential with the most important search engine today...
So, don't forget to fix your site logo's link when you go live, as it's the most hit "home" button.
A better way to implement this is by using this short php code as your link:
<a href="/<?php echo $this->baseurl; ?>/" title="My site's homepage">Your logo</a>
The above code will always print the right path to your site's root, no matter if you're on a dev server or live.
Alternatively, you can add this in your .htaccess file (if you're using it of course):
# Redirect /index.php to / - will also clear /index.php/something to /something
RewriteCond %{THE_REQUEST} ^[A-Z]+\ /index\.php(/[^\ ]*)?\ HTTP/
RewriteRule ^index\.php(/(.*))?$ /$2 [R=301,L]
Use the above code with caution as in some rare cases, it may break your site...
More .htaccess goodness here: http://snipt.net/fevangelou/custom-htaccess-rules-used-on-joomla-sites-we-build/
If you're feeling masochistic, you can always create a Google Analytics account and specifically tell Google that your site's root is index.php so it won't consider domain.com/ and domain.com/index.php as 2 different pages...
Fotis 30 May 2015 
