You may check the CERVUS Software of Parentage analysis (http://www.fieldgenetics.com/pages/aboutCervus_New.jsp). I used the software to analyze pollen dispersal, but the output of the analysis also estimate probability of the NULL allele existence among loci across evaluated population. You may download the newest version of the software using this link http://www.fieldgenetics.com/pages/aboutCervus_New.jsp
FreeNA available at http://www1.montpellier.inra.fr/CBGP/software/FreeNA/ can be used to estimate FST from corrected genotype data for null alleles, while CERVUS for probability of the NULL allele.