exposure - How many EV will a softbox knock down off your flash?

I was shooting on the beach into the sun and using my sb-700 on camera as fill. The camera I was using, a D3200, has a max shutter speed of 1/4000 of a second and no HSS. So, I used an ND filter — I don't remember exactly; maybe ND350ish — to slow down my shutter speed below my native sync speed. (I was metering off the sunset and using flash to expose my subject).

I noticed, however, that when I was using an on camera softbox on top of my flash that even though I was shooting at +3 EV, my exposures were coming out considerably darker than the exposures I did not use a soft box for. Of course, those without the softbox were really harsh and constrasty and rather unappealing.

So, this experience let me to this question: how many exposure value stops should I budget for my softbox? And, more generally, do front diffusers on different softboxes present with different qualities; i.e. different color temperature, different transmittance?