You would seem to be contradicting yourself here.
Nomenclature aside, a small craft damaged a large craft.
I agree. A small craft from the future damaged a large craft. To use a modern analogy, I would not be surprised if a medevac helicopter with a door gunner from today's USAF were able to force a 19th century battleship to strike its colors if they somehow ended up in a firefight.
However, I stand by my original comments. I do not believe that anything in the future is ordained or inevitable or that if someone has fancy technology A then they must have fancy technology B. I will limit myself to what I observe in understanding how things might work in such a setting. As I see things, there is no weapon readily available to anyone but the Borg during Janeway's tour on the Voyager that could be mounted on a shuttle and then disable a functional ship the size of Voyager before the Voyager would have a chance to return fire and overwhelm the shuttle's defenses. I do not equate shuttles to fighter planes. I equate a shuttle to a dinghy.
I am willing to say that if I am wrong, then my theory is invalid. Is there any weapon that could be mounted on a shuttle and disable the Voyager before Voyager could mount a counterattack?