When you match :: you are consuming both colons. Try this using a zero width lookahead:

my $line="root:XXXXXXXXXXXXX:12103::::::";
$line=~s/:(?=:|$)/:NULL/g;
print "\tAFTER\t$line\n" if ( $line =~ /^root:/ );

__OUTPUT__
        AFTER   root:XXXXXXXXXXXXX:12103:NULL:NULL:NULL:NULL:NULL:NULL
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