There's a lot of missing information. How much dynamite? What type of glass and how thick and how was it framed? What type of bronze is the crucifix made of? And I have no idea about the accuracy of what details are given. But I can make some general comments why no miracle is necessary.
Commercial dynamite is not a particularly powerful explosive. There's very little scorching. A couple of candles knocked over, a bent crucifix (more on that later), but everything else nearby seems fine. This all suggests a small blast.
If the dynamite was placed in a flower pot, there would be no significant shrapnel. Beyond the immediate vicinity of the blast, damage would be via concussion.
If the bomb was placed against a hard, vertical surface below the portrait, that would reflect the blast away from the portrait above it and out towards the altar straight into the side of the bronze crucifix stand. As the bomb is below the portrait, any force against the glass would be perpendicular along its strongest axis. Glass isn't as fragile as in the movies. In contrast, the blast went into the side of the bronze crucifix stand at its weakest point. This is like how you can bend a thin metal bar, but it's much more difficult if you push on the ends.
Since the blast appears to have been very small, and in a large room, there would be little over-pressure to damage the glass. The very limited damage further supports this.
"The concussive wave had penetrated the wall, badly damaging the icon of St. John Nepomucene on the other side " is exactly what you'd expect when you place an explosive against a hard surface. This is the spalling effect where the shockwave of an explosion against a rigid surface causes damage to the opposite side without penetrating the material. It would not have been well understood in the 20s, but was later exploited as a weapon.
In conclusion, a small, low quality bomb placed against a hard surface would reflect the blast away from the portrait above it and towards the crucifix. I don't have the space nor license to test this, but I can say no miracle required. Maybe call the Mythbusters.