South Kensington is only closed to the Piccadilly line while the escalators down to those platforms are replaced. The station itself is still open, and Circle and District line trains still stop at platforms 1 and 2.
Though I believe that even if the station was closed, crowding information would still be available despite the lack of passengers, as the crowding API currently uses historical WiFi connection data. TfL do however plan on releasing near real-time data in the summer of this year, so at that point the crowding info would likely reflect any closures.
(source: New WiFi data API)
Unfortunately I am not aware of exact what the percentageOfBaseLine value represents and have been struggling to figure it out myself. Perhaps @jwithers could be of some help here, as they announced the availability of the crowding API.