Sen2Cor is a processor for Sentinel-2 Level 2A product generation and formatting; it performs the atmospheric-, terrain and cirrus correction of Top-Of- Atmosphere Level 1C input data. Sen2Cor creates Bottom-Of-Atmosphere, optionally terrain- and cirrus corrected reflectance images; additional, Aerosol Optical Thickness-, Water Vapor-, Scene Classification Maps and Quality Indicators for cloud and snow probabilities. Its output product format is equivalent to the Level 1C User Product: JPEG 2000 images, three different resolutions, 60, 20 and 10 m.
Source: http://step.esa.int/main/third-party-plugins-2/sen2cor/
So accordingly in case of thick cloud you should apply IdePix, and in this case IdePix is applied on L1C,
Please take a look at the following post,