Your code has a lot of regularity, but you're not exploiting that. You can reduce a lot of potential maintenance headaches by doing so. I'd rewrite it as follows.

use strict;
use DBI;

# Check arguments first
if (@ARGV != 2)
{
    die "Need exactly two args, got ", scalar(@ARGV), "\n";
}

# Set up all our SQL
my $time_sql =
    'select sid, cid from acid_event where timestamp between ? and ?';

my @tab_sql;
foreach (qw(event iphdr tcphdr udphdr icmphdr
        opt data acid_ag_alert acid_event))
{
    push @tab_sql =>
    "delete from $_ where "
    . ($_ eq 'acid_ag_alert'             # this one's different
        ? 'ag_sid = ? and ag_cid = ?'
        : 'sid = ?    and cid = ?');
}

# Connect to the database
my $db = DBI->connect(qw(dbi:mysql:snort acid_user secret))
    or die "Can't connect: $DBI::errstr\n";

# Get outer level data
my ($outer_sth, $inner_sth);
my ($sid, $cid);

eval {
    $outer_sth = $db->prepare($time_sql);
    $outer_sth->execute(@ARGV);
    $outer_sth->bind_columns(undef, \$sid, \$cid);
};

die $@ if $@;

# Loop for each row of data
while ($outer_sth->fetch())
{
    foreach (@tab_sql)
    {
    eval {
        $inner_sth = $db->prepare($_);
        $inner_sth->execute($sid, $cid);
        $inner_sth->finish();            # not really necessary
    };
    die $@ if $@;
    }
}

$outer_sth->finish();         # not really necessary
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Note, I've only tested this to a limited extent since I don't have snort.