$file1{$word}{$site} += $count;

##</code><code>##

use strict;

my %data;
my @filenames = ...;  # @ARGV or literal strings or whatever

for my $fname ( @filenames ) {
    open my $input, "<", $fname or die "$fname: $!";
    load_data( $input, \%data );
}

# doing stuff with %data is left as an exercise...

sub load_data
{
     my ( $fh, $href ) = @_;
     while ( <$fh> ) {
        next unless ( s/^(.*?):\s*// );
        my $word = $1;
        for my $field ( split ) {
            my ( $site, $count ) = split /,/, $field;
            $$href{$word}{$site} += $count;
        }
    }
}