I have used buffers much like the one you describe to make extracts out of fly embryos that include DNA binding proteins (eg Lola and Abrupt). I generally also throw in some NaCl, at least 100mM. Occasionally I have tried increasing the salt concentration (to 250 or 500mM); usually it doesn't make much difference but some proteins may be extracted better in high salt. If I am really concerned, and I only want to run the sample on a gel, I'll include urea in the extraction, but that should not be necessary. The main thing is to be sure you grind the embryos thoroughly. Those little "pellet pestles" that fit in a microfuge tube do work, but they are not the most reliable - many of the embryos sneak around the side of the pestle and never lyse. For protein extracts I generally use an old fashioned Dounce homogenizer, using 20-30 strokes of the A pestle and then of the B pestle. There are also variations on bead beaters and other such devices that use glass, stone or ceramic pellets or grit to lyse the embryos. Anyway, if you can lyse the embryo itself, lysing the nuclei isn't such a big deal.

Thank you very much Edward! I also use the Douncer homogenizer and NaCl at a final concentration at 150mM and for the moment the first attempt has worked well.