don't know if it's that much faster but it's IMHO better readable (i.e. more "perlish") =)

 
  DB<112> @Y=qw(a b a)
 => ("a", "b", "a")

  DB<113> %Ypos=(); $i=0; 
 => 0

  DB<114> push @{ $Ypos{$_} },$i++ for @Y 
 => ""

  DB<115> \%Ypos
 => { a => [0, 2], b => [1] }
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please note that the debugger-shell has problems to handle lexical variables, that's why I omitted them.

And I avoided dereferencing, but I don't think it'll cost you much reintroducing it. (if needed)

But you should add my declarations in productive code.

PS: from 5.14 on you can also write

push $Ypos{$_},$i++ for @Y