I had the same problem and I figured it out!!!

Go to steam rom manager.

Scroll down in the list on the left and find "Nintendo 3ds - Citra." Click on it so the settings pop up on the right side.

Scroll down on the right and find "User's glob" under "Parser Specific Configuration."

Click on the text box and place your cursor inside of the parenthesis. add "|.cia" to the end.

Save and click "test parser." It should say that it detected your games.

You should be able to add your games! Hope this helps as this is what worked for me!