There's a ton of weirdness in every space battle in Trek, and just a few grams of dialogue to explain it. It might be prudent to always assume that the heroes know their trade, and know more than they tell the audience, and that this dictates their sometimes strange-looking actions.
Perhaps only one of the Kazon behemoths was inadequately shielded and could be immediately disposed of? After all, these ships are stolen property, and qualified mechanics with authorized spares are hard to come by; moreover, the ships come from feuding factions, and probably don't share a common pool of maintenance resources. So it would make sense that similar-looking ships would in fact be at very different states of disrepair and combat-incapability.
OTOH, there must be thousands of Kazon aboard each of those ships. Janeway has no desire to kill them all. An early "shock and awe" strike might deter the rest from action, so Janeway would be excused in trying that out first. But once it didn't work, there'd be little point in trying to kill more Kazon.
Timo Saloniemi