The Validity of an Advantage in a Chess Game

Here is a game that I was playing at a chess tournament(I had less than 5 minutes after move 17)

I was analyzing this game afterward with Stockfish and it said that I had an advantage after his 16. Qb4 move. I am not sure that I really have an advantage since a move like Bh3 which the computer recommends can be met by Bh1 and then Nb5 with a plan to go to e4 seems slow because there is probably no attack. How does the move Bh3 give me a better position?

16. qb4 nb5 17. nf3 nd6 (forced because ne5 is coming and the queen cant cover the knight) 18. ne5 and now the queen has nowhere active to go, and the bishop is still doing nothing but guarding the pawn.  

By contrast, bh3 not only trades off your misplaced inactive bishop for his better one, it also frees additional squares for your queen.  Since white's queenside knight and bishop are both difficult to get active in this position, black has a slight but noticeable edge.  

In other words, this isn't really a position where who has an attack is the issue.  Rather, it is about which option gets your pieces the most active, as compared to the enemy pieces.  Its not a huge swing, but bh3 is the better move using this criteria.  

Huh. The thing is my opening went wrong so I thought my position was worse.

Well na6 was bad.  Once you play na6, the knight is not only out of play, it also makes your re8 pointless since the rook cant support e5 without the knight.  Nbd7 was natural.  Other then that, nothing jumps out as a serious mistake on your part.  Just minor positional errors on both sides resulting in a position that the engine likes slightly better for black, but is still more than close enough to be effectively equal for most.  

Nbd7 Nh5?

Thing is, there is no follow up.  So if nbd7 nh5 be6 both the bishop and the knight are on stupid squares.  Which is on a worse square or doing less?  As compared to the game, the difference is your knight is on a better square.  You could also have avoided 8. ... re8.  The problem with re8 there is that its not at all clear you are getting e5 in.  It can be just a wasted move.

I have trouble playing against these Nf3 systems

What should I do against 1. Nf3?

1 Nf3 c5 might not be good if one is not ready for 2 e4. 1 Nf3 d5 is (I think) a common alternative to 1 Nf3 Nf6.

ECO advantage classifications: "stands slightly better", "has the upper hand", and "decisive advantage"

What can I improve on based on this game I showed?