If people have a loose enough definition of Mary Sue that they consider Dash to be at risk of becoming one, then they should really think that of all the ponies. All of them are perfect in their own way. Even Applejack.
Fundamentally, there's nothing wrong with things that lean in the direction of a Mary Sue. Characters can be great at things. They can be the best at things. Good authors can draw from their own lives and even write themselves into their work. It's when these kinds of things are taken too far that it becomes a problem.
As for the Sonic Rainboom, in it's first appearance, it was clear that Dash should be able to do them, because she was born with the right hair type and has actually done one in the past, but something mental was stopping her. Friend in danger? Mental block is broken, she performs her second one.
In it's second appearance, first chronological, we see that she performed one as a child, in her first ever race.
That tells me that it's not something that's physically difficult for her to do, it's mostly in her head. Something happened to her between her childhood and the Young Flyers Competition which caused her to doubt her ability to do another (I'm guessing her lack of flight control, and having made herself a bullying target by standing out), and it was the doubt made it impossible for her to continue doing them. Since she was unable to do a second one, she increasingly was forced to write off her first one as some sort of aberration or fluke. She might even start to doubt that the first one ever happened.
I think it's fine to say that the confidence boost from the second one was all she needed to be able to do them on a regular basis, and I think that it's very much in-character for her to be playing with her new trick.
I suspect that she hit the ground beneath the house, causing the explosion and mushroom cloud. I wouldn't expect her to survive that, but... it's a cartoon and she's made of dark matter.
As for it's usefulness, timing the shockwave to appear just before she hits the ground, allowed her to hit a structurally-compromised building with a point-blank shockwave. It's not clear if it was the Rainboom's shockwave or Dash's impact with the ground (or both) which wrecked the house though. It's not like it matters. Dash was playing. She had to try and hit it with a shockwave.