They are separate variables/constructs. The entry in the hash for key is just a reference aka pointer to the subhash. For example:

my %hash; $hash{key}{subkey}=123;
my $f= $hash{key}; $hash{key}= undef; #moving the subhash
print $f->{subkey}; #would print 123
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Now the code above shows really nothing as this could all be done by internal magic, but in truth internally they are separate too.

BUT... internally nearly everything is separate, even a variable name and its value. Or the hash (which is a big table of "buckets") and the hash values are in separate memory locations, in the bucket is only a pointer to the actual value.