Do flavored coffee beans have calories?

Usually, but if and how many will vary by brand, flavor, etc. You'll need to check the label on the particular flavored coffee you're interested in.

More often than not, you can opt for a sugar free flavored syrup at stores like Starbucks and high end supermarkets. These coffee flavored syrups have no calories. Standard coffee (served black - no milk or sugar) has about 5 calories per cup (6 fl oz.).