The fingerboard is not structural, so the only reason to repair the crack would be aesthetics.
Ebony is highly prone to cracking and checking. It is the nature of the wood. It is highly oily and cures MUCH more slowly than many other woods. The likely reason for the crack is that the ebony has cured out and shrunk. Because it is affixed to the maple, it had to give somewhere.
In addition, because of the very tight grain, it tends to expand and contract very differently than the maple or another wood that it is adhered to during seasonable changes. So, if you fill in the crack, you are running some risks down the road of having created a brand new problem. Similar to what happens when a hardwood floor shrinks in the winter and dirt fills in the seams. When the moisture comes back, it buckles.
In short, leave it alone. It is the nature of things.
If you just CAN'T live with looking at the crack, rub a black grease pencil (crayon) perpendicular to the crack and then buff it off the surface with a rag. It will make the crack all but invisible and squeeze out if the crack tries to close.