You might still disagree with this, but I guess the main thing I mean by efficiency in the case of biology is that natural systems seem to take the shortest route in response to stimuli.

Not necessarily. Evolved systems take the first route available. If a more efficient route is encountered by chance, and proves to be enough of an advantage to win out over the original, then that is where it will continue. But it cannot easily account for situations where that fundamental strategy is no longer viable (particularly if the part is highly conserved), or plan ahead, taking a less favourable strategy for a better one later on.

For example, in mammals, the recurrent pharyngeal nerve is conserved from our fishy origins, looping around the aorta and back up. This was fine in the fish days, where that route was easier, due to the different internal structures, but it is no longer efficient, egregiously so for giraffes and humans, where it extends down the neck, only to go back up again

Since it is a highly conserved vital structure, it is extremely difficult, if not impossible for us to evolve a more efficient path for it to take, even though keeping it all inside of the head would be far more efficient. We might be able to evolve alternative uses for it, but it is a long and convoluted chain that we would need to develop in order to shorten it at all.

I'm not sure that some of those weaknesses of the Borg are really weaknesses.

Data can put a whole cube to sleep

Data had access to a privileged drone. Locutus was acting as a mouthpiece for the Borg, and was a special case, having a name, and having their knowledge be in active use by the Collective.

A conventional drone would likely be overridden by the rest of the Collective, and the Borg would be hard-pressed to allow most drones to go along without a fight.

their ships are subject to easily being infiltrated

That's not really a weakness for the Borg. If you're not trying to attack them, they don't particularly care. They have nothing to hide, and the opportunity would allow them to study you just as much as you are studying them.

It's much the same reason why they don't use cloaking devices, or otherwise hide their presence. The intimidation factor is far more useful.

The Borg may believe in perfection, but I think they are on a fools errand.

They would be, if they were controlling all aspects of the environment, as the nature of the Borg makes internal development difficult. Individuality is not readily acknowledged, and the Borg do not actively try and improve themselves. They are almost entirely reliant on external stimuli to that end.

If the Borg were ever to win, then the galaxy/galactic cluster would stagnate, putting a stop to their ability to develop further, making it an undesirable goal. There is no winning for the Borg, even if they assimilated the entire supercluster, not without major changes to how they work.