but get Undefined subroutine &main::crypt

This is because prepending subroutines with an ampersand forces a user defined function to be called. If you're really determined to override the default prototype, you could just subvert crypt with the subs module e.g

use subs 'crypt';

sub crypt { CORE::crypt($_[0], $_[1]) }

print crypt( (time) x 2 );
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For a good rant^Warticle on prototypes in perl see Tom Christiansen's FMTEYEWTK about Prototypes in Perl.