Objects in Perl are references anyway, specifically blessed references. Therefore when you pass an object to a subroutine you are necessarily passing by reference. For example, in the following snippet $obj is passed by reference and may be altered by munge_it()

my $obj = Some::Class->new ();
munge_it ($obj, $data);
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No copying of objects should have occurred here.

If you want to know why your script is slow, profile it. Much better than guessing and spending time "optimising" some part of the script which doesn't require it.

Good luck.