Something that's been bugging the hell out of me, can a station run out of a commodity if the user or player buys too much of a singular item such as a mil or more?

No.

Not right now, but we're planning to experiment with this kind of thing in grayspace.

It adds a great deal more complexity to things, as you have to scale availability based on current population and usage. Otherwise you get a crap user experience for a lot of confused newer people.

So, instead of that, we'll probably keep infinite-supply in the core nation space, and introduce limited supply in more outlying regions.

That would justify the existence of traders. If that would ever be implemented...