1. Given that I want to study the distribution of these x and y points on each detector in each observation, what would be the best structure for this data?

I'd suggest a HoHoAoH (see the spoiler below) :-)

2. What do I study so I can better see such things (e.g. how do I get there from here)? Are there general books on data structures, or will this knowledge just come with experience?

There are books on data structures, but real knowledge only comes from experience.

3. Is it okay (I know, "according to whom?") to utilize solutions/tools/schemata one does not yet truly understand, and hope for enlightenment to come later?

That's a decision for you to make. But without the understanding, how do you expect to make even trivial changes to the code?

4. There is no number 4. Note I am studiedly avoiding asking "so, now do I create the structure suggested by (1)?"