One possible solution is to build your hash as a tree (that is a nested hash) in the first place:

my %freq = (
   aa => {
         a => 5,
         b => 2,
         c => 8,
         ...
  },
  ab => { ... },
);
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You can then get all two letter prefixes with a simple hash access. If you want to access one-letter prefixes as well, nest beginning from the first level instead.