in reply to structuring data: aka walk first, grok later

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)?" 
use Data::Dump 'pp'; # a "better" Data::Dumper

my %obs;
while ( <DATA> ) {
    chomp;
    my ( $obs_num, $det, $x, $y ) = split;

    push @{ $obs{$obs_num}{$det} }, { x => $x, y => $y };
}

#$obs{$obs_num}{$det}[$reading]{x}

pp \%obs;

__DATA__
21 DET-2 896.657564735788 678.83860967799
21 DET-3 32.0939023018969 621.656550474314
21 DET-3 42.0741462550974 834.842294892622
21 DET-3 218.814294809857 450.606540154849
21 DET-3 228.88830316475 625.939190221948
21 DET-3 630.472705847461 220.839350101088
21 DET-5 152.988115061449 156.31861287082
88 DET-0 114.871177986263 212.959076023136
88 DET-0 219.421725079137 710.314439572696
88 DET-0 257.837516726887 594.376577764894
88 DET-1 119.630462310966 260.433234269099

[download]

Output:

{
  21 => {
          "DET-2" => [{ "x" => "896.657564735788", "y" => "678.8386096
+7799" }],
          "DET-3" => [
                       { "x" => "32.0939023018969", "y" => "621.656550
+474314" },
                       { "x" => "42.0741462550974", "y" => "834.842294
+892622" },
                       { "x" => "218.814294809857", "y" => "450.606540
+154849" },
                       { "x" => "228.88830316475", "y" => "625.9391902
+21948" },
                       { "x" => "630.472705847461", "y" => "220.839350
+101088" },
                     ],
          "DET-5" => [{ "x" => "152.988115061449", "y" => "156.3186128
+7082" }],
        },
  88 => {
          "DET-0" => [
                       { "x" => "114.871177986263", "y" => "212.959076
+023136" },
                       { "x" => "219.421725079137", "y" => "710.314439
+572696" },
                       { "x" => "257.837516726887", "y" => "594.376577
+764894" },
                     ],
          "DET-1" => [{ "x" => "119.630462310966", "y" => "260.4332342
+69099" }],
        },
}

[download]
Unless I state otherwise, all my code runs with strict and warnings

In Section Seekers of Perl Wisdom