As long as the effect is projected from the invisible caster, yes
Greater invisibility states:
Anything the target is wearing or carrying is invisible as long as it is on the target's person.
When you are casting a spell that projects an effect (like fireball or lightning bolt) you are not wearing or carrying the effect and that effect is certainly not on the caster's person. This means that the effect becomes visible as the caster casts it. And since you can now see the effect, danger sense applies.
However, if the effect is not projected from the caster, and the DM rules that the effect fulfills the requirement above, then danger sense wouldn't apply since the magical effect itself would be invisible. I have never seen a spell combine with greater invisibility in that manner though.