It doesn't look like each folder has all the files for every game. From what i can see, it's only the folders with more empty folders inside them.
Right, this is by design to simplify maintenance of these older products, the disk usage is small (For this day and age.
Nothing extracted yet.
It looks like the HL1/CS Linux depots seem to contain all the HL1 based games.
There are directories for bshift, czero, dmc, dod, gearbox, ricochet and tfc in my CS 1.6 install.
Imagine you're installing all these games in Steam, and they all contain each other, that's going to take a lot of hard drive place.
There are also a lot of ".dylib.dSYM" folders which seem to be empty.