One common symptom of having a hacked Joomla site is unusual slowness. If your site is a little slow, it's not as likely that you've been hacked. However, if when you load a page you experience a sudden increase in load times of 6 to 20 seconds, it's likely that your site has been compromised. Another symptom that you've been hacked is when the slowness only affects the front of your site and your Joomla control panel loads quickly.
The situation can be a little bit bewildering- what is going on here?!