If you want to knock down a gene to learn about its function, it can be useful to assess the loss of function without a background of altered gene expression due to compensation. Now there are data showing that mutants can compensate and the response differs from that of morphants.
Rossi A, Kontarakis Z, Gerri C, Nolte H, Hölper S, Krüger M, Stainier DYR. Genetic compensation induced by deleterious mutations but not gene knockdowns. Nature. 2015;[Epub ahead of print] doi:10.1038/nature14580
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14580.html
Hesman Saey T. Mutation-disease link masked in zebrafish. ScienceNews. 2015;July 13
https://www.sciencenews.org/article/mutation-disease-link-masked-zebrafish