The code you have works properly on undef values:

#!/usr/bin/perl

use vars qw(@day);

$day[5] = '';
printday();
$day[5]="\n";
printday();
$day[5]=undef;
printday();

sub printday
{
  my $len = length($day[5]);
  if ($len =~ /8/) {
    print "$day[5]";
  } else {
    print "00:00:00";
  }
  print "\n";
}
[download]

outputs:

00:00:00
00:00:00
00:00:00

as expected. So there error is likely to be elsewhere in your code.

Using $len =~ /8/ to see if the length is 8 is very strange. It says "if the string representation of the length contains the digit 8", so will match 8, 18, 3008, 8000000, etc. You probably just want $len == 8.