It's a simple case of refactoring. I really dislike duplication, since duplication is just asking for bugs. As a note, it seems you're writing to FIL before you open it.

if ($ct > 0)
{
     open(FIL, ">>$myfil") || die "Write to $myfil failed\n";

     print FIL "\n$ct ";
     print FIL ($ct > 1)? "are not available" : "is down";
     print FIL " at this time.\n";
     close (FIL);

     system("mailx -s 'Mail Header' myemail < $myfil");
}
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Note that you should probably be using something like Mail::Mailer or Mail::SendMail to do the dirty work of sending mail.

In your original code, if your e-mail address changed, you'd have to do twice the work to update it, and further, there is a chance you might miss one of them.

When handling simple pluralization, like what you have here, the ?: operator comes in handy. If you're not familiar with it, here's how it works:

print "\$foo is ";
print $foo? "true" : "false";
print "\n";
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Or you can compact this to something like so:

print "\$foo is ",($foo? "true" : "false"),"\n";

More idiomatically:

print "There ",(($num == 1)? "is" : "are")," $num camel",
       (($num == 1)? "" : "s")," for sale.\n";
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Or perhaps something more "Old School":

printf("There %s $num camel%s for sale.\n",
       ($num == 1)? ("is","") : ("are","s"));
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