Thanks Ikki for the question,
TheList determines encryptions based on what is defined in the PMT (Program Map Table) PID when scanned in by a FTA receiver.
Iceberg and USDownlink have given the main reasons why the encrypted channels are listed (Channels can go into free preview mode, and some satellites do not have FTA channels on a certain polarity) a few other reason are:
It can be helpful to identify a satellite when aiming your dish.
Also it can give you a general idea in the video quality of a channel, for example if encrypted channels are not listed, then I would think that TV Romania is the only channel on G19 11934 H 20000 and I might expect the channel to have a very high video quality (high bitrate), but because encrypted channels are listed I can see that it shares the 20000 symbol rate with 8 other TV channels plus a few radio channels, and I would not expect the quality to be as high as I expected before.
However encrypted channels are not listed on the subscription satellites to keep hackers away and because there is a special section that contains more useful information for subscribers. Most subscribers do not care about frequencies, pids and encryptions. They care more about transponder numbers, modulations, channel numbers, packages and whether or not their provider has made a channel available to them.
I hope this makes sense, I am a bit tired because I am trying to push the new version of TheList out sometime this year
By saying this hopefully it will get done quicker.