1) At that level, does the difference between 99.85 and 99.90 come down to luck?
I'm not entirely sure how best to answer this question, but there is certainly a lot of luck involved. The difference between, say, a 47 and a 50 is, in actuality, negligible, especially in the field of humanities, where markedly different conceptions of the good exist. Your study score for a subject like English depends, in no small measure, on how your marker is feeling whilst he or she is marking your paper, and whether or not your writing style is to his or her taste. I know VCAA implements an array of measures in an attempt to reduce subjectivity, but the system is not infallible.
2) Do many universities offer scholarships for anything less but this score? Especially residential options (except disadvantage scholarships and etc).
As people have mentioned above, Monash offers a whole range of scholarships. You do not have to get 99.90+ to get a scholarship from Monash. Unfortunately, however, this is not the case with Melbourne. Unless you are eligible for SEAS, if you don't get 99.90+, the chances of you getting a scholarship will be very slim.
3) Those who did get it, in what parts do you think it came down to natural ability, hard work and luck? (like 3/4 hard work etc)
As much as the term is bandied about, I don't believe there is such a thing as 'natural ability'. When people say a student is 'naturally talented', they usually mean that the student is very quick at understanding things and absorbing new material. But this skill, if you will, is, IMO, not acquired from birth but acquired through habituation. Those who have been exposed to certain things which so happen to pertain to a particular subject area will inevitably find that subject area easy. For example, students who have been exposed to the history of an array of countries from an early age will inevitably find history easy, since they will inevitably be more able to draw certain historical links in their heads and make sense of evidence presented before them. It is not as if certain humans were born with special 'capacities' already ingrained in their minds. I subscribe to the tabula rasa doctrine; we are not born with any mental objects (I'm using this term as a technical term).
Anyway, I digress. If we were to take 'natural ability' to mean 'the product of targeted habituation', then I think that hard work is, by far, the most significant of the three you mentioned above. VCE tests are NOT intelligence tests. The students who get the highest scores are, by no means, the smartest students, if we were to take 'smart' to mean something along the lines of 'perspicacious'; they are simply the students who know the syllabus most thoroughly. Of course, in order to gain a thorough understanding of the syllabi set by the VCAA, students need to work hard and put in the hours. Although 'targeted habituation' may help to speed up the learning process (if the student is lucky), in the context of VCE, it is never enough to carry the day.
4) What opportunities does it open up, and are these opportunities worth the amount of work that goes into this score?
Yes. And yes. The scholarships you get offered for scoring 99.90+ come with a whole array of perks, which you can look up for yourself on the Monash and Melbourne University websites. The hard work definitely pays off. I had a friend who literally slept for an average of 5 hours a day. Although I definitely do not suggest that you do this (health is more important), but it all paid off in the end, because getting that sort of ATAR opens pretty much all the doors available to be opened (some unis take into consideration UMAT scores, etc. but yeah...)
5) Basically, should I make it my aim for next year? I suppose most people who do so are disappointed in the end. (I'm almost definitely going into MelbArts, but maybe Monash Arts/Law)
I'd definitely suggest that you make it your aim for next year if you believe that you have the ability to achieve it. As they say, always better to aim high and fall amongst the stars than to aim low and end up a mere 3 steps higher than your aim.
One last thing. While it is good to work hard, don't lose sight of everything else in life. Your ATAR is literally NOTHING MORE than a ticket to tertiary education. Getting a high ATAR simply means getting a more versatile key. That is all. You should not treat your ATAR as though it were your life. Try to maintain something that resembles a social life, and continue with all or most of the extra-curricular activities you have been participating in before year 12. You don't want to walk away with any regrets.
Hope this helps and good luck!