This will depend on how you extract the DNA, but fresh sample is almost always better than frozen.  Which kit / protocol do you use for extraction? Do you freeze the embryos in any storage buffer? 

5dpf single embryo?My experience is that  they  already come out!

I routinely freeze (frog and lamprey) larvae in DNA extraction buffer at -20 deg C for up to 2 years before finishing the extraction. Those provide me with more genomic DNA than I will ever need -- I should think your frozen samples would be just fine.

Anecdotally, I know a genetics professor that has successfully genotyped mtDNA of fish filets that were purchased from a grocery store. Granted mtDNA is present at a higher copy number per cell, and not all filet samples worked, I still think this goes to show that DNA is pretty resilient in general.

Let us know!