Cecilia Jarlskog proposed this invariant already in 1973 and it was mentioned in the original Kobayashi-Maskawa paper.
For three families, it's easy to see why it is nonzero iff the unitary matrix in $U(3)$ can't be brought to the real, orthogonal i.e. $O(3)$ form. It's because after the 5 phase redefinitions of the up-type-quark and down-type-quark eigenstates, every $SU(3)$ matrix may be brought to the form of an $SO(3)$ matrix expressed by 3 real angles $\theta_{ij}$ and a single extra complex phase $\delta$, well, I mean $\exp(i\delta)$, added to a matrix element.
In that parameterization of the $SU(3)$ matrix, the invariant is simply
$$ J = c_{12}c_{13}^2 c_{23}s_{12}s_{13}s_{23}\sin \delta. $$
Note that it vanishes exactly if at least one of the factors is zero which means either if the complex phase $\delta$ is zero or $\pi$ mod $2\pi$ – then the matrix is explicitly real orthogonal and CP-preserving – or if any of the sines or cosines of the angles vanish in which case it's also possible to bring the matrix into a real form.
See
http://physics.brown.edu/physics/undergradpages/theses/2010Theses/GoldfarbThesis_Final.pdf
especially pages 7, 8, 11, 12 for some details and formulae. In particular, the first "standard" formula on page 7 makes it clear that the $SU(3)$ matrix is real – or can be made real - whenever one of the factors in $J$ vanishes.
EDIT:
The added questions have nothing whatsoever to do with the original one but they may be answered, too. There is no "constructive way" to derive the Jarlskog invariant. It was a clever guess, a proposed convention. A quantity that is zero whenever it should be is clearly not defined uniquely.
Also, it is incorrect to expect a canonical generalization to larger unitary matrices. Moreover, larger matrices actually have several independent sources of CP-violation, in the same sense as 2 x 2 matrix for 2 families has none. So it would be more natural to have several invariants for larger matrices and say that CP is preserved if all of them are zero. But once again, those invariants wouldn't be unique in any sense.
Concerning the third question, independence on bases, it's trivial to see. The CKM matrix $V$ is the transition matrix mapping three particular mass eigenstates to the $SU(2)$ partners of three other particular eigenstates. All these six eigenstates are determined uniquely, up to a phase (assuming they're normalized).
But it's easy to see that $J$ is invariant under these six changes of phases. For example, change the phase of the $b$ eigenvector by $\exp(i\beta)$. This phase gets cancelled in $J$ because $J$ depends on this phase only via $V_{cb}$ and $V_{ub}^*$ factors: in both of them, $b$ is the second index so the dependence on $\beta$ is the same but the second matrix element is complex conjugated so the phase cancels. Similarly one may verify the cancelation of the five other possible phases and that proves the independence on the basis.