The distinction between these two equations is that: $p+ \rho u^2=constant$, is valid only for 1D compressible flow while, $p+(1/2) \rho u^2=constant$, is valid for incompressible flow.
The difference arises because of the coupling of continuity and momentum equation in compressible flow. This coupling is absent for incompressible flow. You can see this by a simple derivation from 1D Euler's equation. Euler equation is basically the momentum equation where the viscous forces are neglected.
$$ \frac{dP}{\rho}+ u du + gdz = 0 $$
Let's also neglect the body forces. Now this becomes:
$$ dP=- (\rho u) du $$
Where P is the pressure, $\rho$ is density and u is the 1D velocity. This is valid for both compressible and incompressible flows. For deriving the Bernoulli's equation, you simply integrate both sides.
$$ \int{dP}=- \int{(\rho u) du} $$
If the density, $\rho$ is constant, flow is incompressible, and you can take $\rho$ out of the integral sign to get your Bernoulli's equation.
$$ P= -\rho \int{u du} = -\rho \frac{u^2}{2}+constant$$
$$P+\frac{\rho u^2}{2}=constant$$
Now, consider the case of compressible flows. Here you cannot take the density $\rho$ out of the integral. Instead, you can use continuity equation for compressible flows, which says: $\rho u=constant$, to take $(\rho u)$ out of the integral. So, we have
$$ P= -(\rho u) \int{du} = -\rho u * u+constant$$
$$P+\rho u^2=constant$$
You see? We had to use the continuity equation in order to get this. This is the coupling I'm talking about. Even if you derive the 1D compressible flow equation using a control volume, using $P_1 , V_1 ; P_2 , V_2 $ at entry and exits, you'll still need to use the continuity equation $P_1 V_1 =P_2 V_2$ to get $P_1 + \rho {V_1}^2=P_2 + \rho {V_2}^2$. The derivation from Euler equation just helps to see the distinction very easily.