You could use a single hash, using the Ob2 value as key, and a counter as the value. Keys that end up with a value of 1 are unique to a single Ob1, while keys with a value greater than 1 are common to both.

Here's some code:

#!/usr/bin/perl
my %ob2;

while( <DATA> ) {
    my @v = split;
    $ob2{ $v[3] } ++;
}

print "Duplicate Ob2: ",
    join ', ',
    sort grep { $ob2{ $_ } > 1 } keys %ob2;

__DATA__
HIT object1 563.43.78 object3 123.89.7777
HIT object1 563.43.78 object10 123.89.7777
HIT object1 563.43.78 object2 453.78.122
HIT object1 563.43.78 object5 457.8888.1
HIT object1 563.43.78 object4 123.89.7777
HIT object1 563.43.78 object6 566.2222.11
HIT object2 563.43.78 object3 123.89.7777
HIT object2 563.43.78 object7 456.222.1111
HIT object2 563.43.78 object8 990.7777.66
HIT object2 563.43.78 object5 457.8888.1
HIT object2 563.43.78 object13 123.89.7777
HIT object2 563.43.78 object9 1223.333.111
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That prints:

Duplicate Ob2: object3, object5
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