Can a casual comparison of phenomena and assumptions based on it be presented in a journal/conference paper?
In comparison to the size of the universe, humans on earth are like bacteria on a speck of dirt. Much like in the animated movie "Horton hears a who"... There might be a civilization of creatures living on specks of dust that we see everyday.


I think the example you have chosen here is obscuring your real question. It's not clear that this example makes any scientific sense, so if I saw this in a computer science paper I would find it very strange and probably suggest that the authors delete it. But your real question is about some hypothetical opinion, not about the (scientifically indefensible) suggestion that there are entire worlds on specks of dirt.

So, to the question I think you wanted to ask: it is OK to write casual comparisons if the comparison is useful and illustrative. Not all arguments have to proceed with a hypothesis test or linear regression or something. Your job is to convince the reader of your hypothesis; the argument for that can be heuristic, philosophical, or on a totally meta level. If it's a compelling point of view and the reviewers buy that it is plausible, they will likely be happy with your paper.


  Observable Phenomenon: The universe is 92 billion light years in diameter. In comparison, the Earth is a mere 12742km in diameter, and the average human height is 1.7m and viruses can be just 20 nanometer in diameter.
  
  Our hypothesis: If the Earth could be assumed as a universe, it may very well be possible that there may be an entire civilization of creatures living on atoms or electrons.


Assuming that the "Observable Phenomenon" and "Our hypothesis" are replaced by something less ridiculous, this seems entirely fine. You are starting with some quantitative observations, and asking the reader to draw a conclusion about some hypothetically possible scenario.