my %lists_by_size;

# get list of file names into @inp_files

for my $file ( @inp_files ) {
    my $group = get_page_count( $file );
    push @{$lists_by_size{$group}}, $file;
}

for my $group ( keys %lists_by_size ) {
    # open output pdf (or output zip file) for this group
    for my $file ( @{$lists_by_size{$group}} ) {  # use sort here if you like
        # append this file to the output
    }
    # close the output
}