You are forgetting that size doesn't matter too much in Trek.
They are able to pack large amounts of energy discharges in small sized objects.
Given similar types of technology, size is the most obvious criteria by which they may be compared. Both the NX and the Danube generate power by the annihilation of matter and anti-matter. The Danube's reactor, as illustrated in the DS9TM--and we may assume this is roughly correct--is orders of magnitude smaller than that of the NX. That means less redundancy, less fuel, and--perhaps most importantly for this scenario--a smaller volume in which the M/AM reaction may take place. Less reaction space limits all kinds of tactically relevant systems on the Danube: energy weapons, shields, inertial dampening, structural integrity, and the console explody devices.
Assuming for the sake of discussion that the DS9TM is also correct about the scale of microtorpedoes that are standard aboard the Danube, again, both ships' torpedoes work by M/AM annihilation and their size limits their efficacy. The power level of the standard photorp is given as ~65 MT in the TNGTM, and fluctuates wildly in the show. Let's be generous give a standard photorp 650 MT. Photonic torpedoes are about the same size, but probably less efficient due to A photorp shell is very approximately 1 cubic meter. I don't have my DS9TM, but ISTR the microtorpedo being about 15x5x5=375 cubic centimeters, or about 1/2667 the volume of a photorp. Assuming a utorp holds the same "stuff" as a photorp, we can (generously) assign it a yield of 0.25 MT. Unless my math is way off (probably is). Either way, there's only so much stuff you can fit into a given space, and that difference eventually becomes meaningful.
The shields of USS Defiant from Kirk's era was able to withstand weapons from multiple enemy targets without problems.
Granted, that was a Constitution class vessel.
Shields from a century later though would be able to do such a thing even better.
Shields from a century later may be more efficient, but that increase in efficiency may be canceled out by a decrease in raw power.
The Danube has the advantage of automation and self-repair.
Did they subcontract their runabout construction out to the Borg?
To address the Excelsior-Defiant match mentioned elsewhere, this is just more evidence that reactor size can help determine the outcome of a fight. The Defiant's MARC is about the size of that of a GCS, maybe bigger IIRC. The little ship was explicitly overpowered. This overpowering is what lets Defiants take on Excelsiors and Negh'vars and survive. Not the fact that it simply has better tech. Apply the same lesson to the Danube: It may have better tech, but it follows the rules that the Defiant broke--it has a much smaller powerplant, ultimately limiting the amount of combat power it can apply and withstand.