in TBOBW we learn the cube atmosphere is perfectly fine for a normal human.
That is, it's fine for Picard. Was that the reason, perhaps?
It's only in VOY that we get a sampling of Cubes or other Borg ships that are not bending over backwards to accommodate human guests. But even there, only ships that have been badly hurt are successfully boarded by our heroes, and only for a short time. Perhaps the air inside indeed is horribly stale to the human tastes?
And in theory earth did not have a very large population after WW3 ended
We only heard of 0.6 billion people dying (and earlier in "Bread and Circuses", Spock had claimed it was only 0.037 billion). That wouldn't be much of a dent in today's population - some wars have done much worse than decimate (in the sense of killing off one in ten) the nations involved.
One wonders what Earth's population in the Trek 2050s was. Lower than ours today or at that date, due to success in birth control or a series of previous calamities? Higher than ours today or at that date, due to such improvements in food production, sanitation and medicine that our reality will not achieve?
As for ships, when the Borg assimilate one, they gradually transform it into a cube. We see this happening with the Earth transport in "Regeneration" (ENT). It's halfway to being a cube by the time it's destroyed.
This also explains how Wolf 359 victims ended up in the Delta Quadrant, and why the Borg spent so much time on that site after the battle that the E-D was able to catch up...
Timo Saloniemi