...But as said, there's no known rule against beaming out
through shields, like Tuvok does there.
The "tiny windows in shields" thing is sort of confirmed in episodes like "Preemptive Strike": there can be weaker sections in shields, and these can be deliberately made weaker still. But using these for transporting people from outside to inside would be such an obvious thing to do that it's unlikely to be the explanation for occasional
beam-ins. Rather, it should happen all the time if it were possible.
How many times did VOY have these beam-ins in the middle of a battle? Five, six? But never without cuts in the action, apparently - these were all cases of the transporting taking place in its own scene, while the camera was necessarily pointed away from the fighting Voyager
, from her exterior, from her bridge. And never of the more damning type where the camera stays on the bridge, our heroes read out shield percentages, and on the background somebody calls a beam-in.
So we can always pretend the shields were dropped for the crucial few seconds; it's just a matter of determining how certainly in each case this would have resulted in Janeway getting her bacon nice and crispy.