The point of 1.Nh3 is to force black to play the more damaging move ...h6 instead of ...f6. This is a strong point in favour of white, especially with the positional 2.d4 followup, instead of the older 2.e3.
1.Nh3 h6 is a perfectly normal opening in atomic; tactics play a larger role in dictating opening moves in atomic than in orthodox chess. 1.d4 looks "normal" but is not as forcing as 1.Nh3.
General opening ideas
In atomic there are two main kinds of openings: those with piece centres, characterised by minor pieces in the centre and generally lots of tactics (e.g. 1.Nf3 f6 2.Nd4 Nh6 3.e3 Ng4); and those with pawn centres, with fewer tactics but greater tension and positional play (e.g. anything with white e4/d4 vs black d5/e6). 1.Nh3 h6 2.d4 falls into the latter category.
Typically in this kind of game, pawns occupy the centre rather than pieces. There will usually be pawns on e4/d4 vs e6/d5 (sometimes e5/d5). In these positions, the knights are naturally developed on the edges, further from the tension in the centre. (Tactics may sometimes allow them to be developed centrally.)
If white plays skillfully, black will always be on the back foot in this kind of opening, cramped and under severe pressure. In the absolute worst case, white has Na3/Nh3 while black has a6/h6, and three of black's minors are still on b8/c8/g8 with no prospects. (Side note: black's c8-bishop can be a thematic problem piece with the d4/e4 vs e6/d5 centres.)
Why is ...h6 bad?
There are two reasons why ...h6 is more often worse than ...f6.
First, in light of the general ideas above, the goal of 1.Nh3 h6 is to prevent black's knight from going to h6. 1...h6 is a necessary evil since 1...f6 2.Nc3 is too good for white. (Side note: I have played 1.Nh3 f6 2.Nc3 Nh6 with some success against 2000 rated players, but it's objectively bad, and more of a mixup to see if my opponents know how to exploit it.)
With h6 blocked, it becomes difficult for black to develop the g8 knight. Ne7 is generally bad and needs another move, while Nf6 is hard to make work. Black will therefore suffer more in the middlegame trying to solve piece activity issues.
The other reason why ...f6 is better is that it creates luft around the king. With f7 empty, moves like Ng5, Ne5, Bc4 and Qb3 do not come with tempo against a king on e8 or f8. This seems like a small point, but can affect many tactical sequences in the middlegame.
In fact, white will often play f3 unprovoked in this kind of Nh3-d4-e4 game, because it's simply a useful move. This kind of move is commonly part of a buildup to a decisive white break in pawn-centre openings.
Blocking the d1-h4 diagonal (white; d8-h5 for black) is not an issue; the queen may go out via a4, b3, or even stay happily on d1.
Likewise, one idea black can try in 1.Nh3 h6 games is to play ...f5 and ...Nf6. Black may have to accept a N for P trade, or even material loss (N+P for P), but can generate some dynamic play in return. (N or B for P is not really material loss in atomic.)