Well, the common theme for all the moves you mentioned is "improve your worst piece".
1) we have a position where, as you correctly mentioned, black's pieces don't have too many options. However, it is more important to note, that White's pieces don't have many options either! In other words, it means that black has all the time he needs to slowly improve his position, since white has no real plan. I think that h6-->g5 is fairly logical. It's not so much about planting the knight on f4 but rather about establishing dominance over the dark squares in general. The knight probably won't stay on f4, it might venture back to g6 and from there have both f4 and e5 open, etc. In other words, black has a ton of time, so he finds a way to improve his position and give his pieces more options without risking anything (any kingside breaks are not scary, black does have more pieces after all!)
2) this one again is "improve your worst piece" theme. The rook on c8 is now doing absolutely nothing and since, again, white doesn't really have anything constructive to do, this is good time to put it on a semi open file. It is not about defending the knight at all, it's about "when the knight moves, rook puts a ton of pressure on the pawn". As a matter of fact, Nc3 is already an immediate threat.
3) what is white's glaring weakness in this position? It's the dark squares. The only piece that can sort of take care of it is the dark bishop. If black can trade the dark bishop in a right scenario (where white rooks can't immediately come over the d-file), white will be completely screwed because of all sorts of outposts (knight to d4, etc). In the mean time, it just takes care of the unpleasant pin and exerts a lot of pressure on that diagonal, making even stuff like h5--> h4 possible and unpleasant for white.
4) again it is about improving the pieces imo. After g3 was played, queen doesn't have much to do on that diagonal anymore. From e7, it defends g5 for possible h5-h4 later on and also has an interesting square at f6 to go to if needed, putting pressure on f3 and a1-->h8 diagonal to assist possible knight jumps (which would then open the a8 rook).
Hope this helps