There will be a lot of damage, both from the sonic boom and the winds
First, the speedster is causing localized winds that in his immediate vicinity are about as fast as he is, 343 m/s. An F5 tornado tops out around 140 m/s. The area of increased winds from the speedster will be smaller than an F5 tornado, but far more intense. These winds will definitely be enough to smash windows and tear up street signs, and hurl the goons off their feet. Certainly there is the potential to structurally damage a building if he runs through it, particularly if the building would not stand up to a tornado. A wooden house would probably be ruined if he ran in the front door and out the back.
The damage from wind is mitigated by the fact that the speedster is only in one location for a very short period of time compared to a tornado (unless he deliberately runs in circles). It's hard to say if he'd be flipping cars just from running past them, but I'm guessing he isn't due to the short duration.
Next we have the sonic boom to contend with. A sonic boom is just a shockwave, and if a shockwave is intense enough it can injure or kill you. The shockwave from a concussion grenade can kill you. Conversely, if the shockwave is not very intense, it will cause no harm, like the shockwave from a firecracker causes no harm. So we have to determine how intense the sonic boom is to determine the likelihood of injury. For this we need to do some physics calculations.
First, we need to know how much force the speedster is exerting on the air. This is his drag force. Since he is running, he's in a position relative to the wind similar to a skydiver in the prone position, putting his coefficient of drag ($C_d$) around 1.
Except he's going a lot faster than a skydiver. Take a look at the chart on page 1 of this document about ballistics. As the projectile approaches the sound barrier, its coefficient of drag sharply increases to three times or more its value at slower speeds. We might guess that the speedster's coefficient of drag at Mach 1 is therefore more like 3, rather than 1. This might be a bit too high, but the speedster's arms and legs will be moving even faster than the rest of him and adding even more drag, so $C_d = 3$ seems like a reasonable guess.
The drag force $F$ is given by the formula
$$F = 0.5 \rho u^2 A C_d$$
Where $\rho$ is the density of air (1.205 kg/m^3), $u$ is 343 m/s, $A$ is the frontal area of the runner (about 0.7 m^2), and $C_d$ is around 3.
F = 149 kN.
To calculate the intensity of the speedster's sonic boom (plus the wind) at 3m distance, we can look at the energy he applies over a distance d, which is F * d, and divide it by the area of the cylinder at 3m distance from his path over d, which is 2 * $\pi$ * 3m * d. The result is 7905 J/m^2.
For comparison, a MK3A2 concussion grenade has 226.8 grams of TNT and an effective casualty radius of 2m in an open area. At the maximum 2m casualty distance, the energy intensity from this grenade is 18878 J/m^2. This is more intense than the speedster's sonic boom, but not by that much.
We can therefore say that being subjected to the speedster's sonic boom at 3m distance is similar to standing a bit outside the effective radius of a concussion grenade. The goons are likely to be injured from the sonic boom, though not necessarily killed or disabled.
They certainly could be killed or disabled if the winds and shockwave smash their head into the corner of a table, or if they are struck by rocks and debris that were kicked up by the shockwave.
These rocks and other flying debris could potentially kill people at much greater distances. That's a hazard with concussion grenades as well, though it's somewhat unusual.
Burst eardrums are a given.
If the speedster and goons are indoors, the shockwave itself would become lethal at 3m because the sonic boom reflects off the walls and strikes the goons multiple times. Same as we see with concussion grenades.
