If you know the set of methods you'll need to query, you could check before any of your methods are installed. 
package MyPackage;
use base "Whatever";
our $can_foo;
BEGIN { $can_foo = 1 if MyPackage->can("foo"); }
sub foo { 'Whee!' }
sub check { return $can_foo; }

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Update: But in direct answer to your question, this (surprisingly) seems to work: 
MyPackage->can("SUPER::foo")

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In reply to Re: Detecting Overridden Methods by sfink
in thread Detecting Overridden Methods by Ovid

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