Is there any way to tell if you found all clues?

In the options menu, you can specify whether or not you want feedback/help with the investigation sections. The main one you'd be interested in is the background music, which will turn off the "investigation music" in a scene when you've found all the clues.

There is also a chime that plays for each clue, and it changes depending on whether you're near an examined clue versus a clue you haven't. If you are playing on a console, there is an option to turn on or off controller vibration when you are near a clue.

Some people prefer to have these options on to assist them during investigations, but others prefer to have them off to increase the challenge and/or the realism.

When you are investigating an area that contains clues, background music will play. Once you have found all clues, the background music will stop.

Really late answer, but I'm putting it here because I can't believe this was never pointed out before!

To tell if you have found everything and can move on, just open your notebook and go to the Intuition page. If the Show All Clues option is gray, it means you've found all clues!

This is the surest way to know if you've found all clues before moving on, because sometimes game-bugs can cause investigation music to continue playing even after all clues have been found.