Consider the momentum balance equation for a steady inviscid flow
$$\int_S \rho \mathbf{v}(\mathbf{v}\cdot\mathbf{n})\ dS = -\int_S p\mathbf{n}\ dS\ +\ \int_V \rho \mathbf{g}\ dV\ +\ \mathbf{F}$$
where $\mathbf{F}$ are other forces.
In my fluid mechanics course the professor said that in a flow the hydrostatic pressure distribution balances the weight of the fluid and therefore we could cut the weight term as long as we used relative pressures.
$$p = p_H + p'$$ $$\nabla p_H = \rho \mathbf{g}\ \text{[definition of hydrostatic pressure]}$$
Applying this would yield
$$\int_S \rho \mathbf{v}(\mathbf{v}\cdot\mathbf{n})\ dS = -\int_S p'\mathbf{n}\ dS\ +\ \mathbf{F}$$
There are two things that are confusing me. The first one is that we were taught that relative pressure was relative to the atmosphere, and the professor seems to be using that same concept in here, but I do not see any reason to why the hydrostatic pressure would be equal to the atmospheric pressure.
For my other question, consider a flow along a horizontal tube, with some flow device in the middle which makes the inlet and outlet pressures differ. Applying the momentum balance in the vertical direction we have both weight and hydrostatic pressure, so they cancel out. However, in the horizontal direction we do not have weight, but we will still have hydrostatic pressure, which does not cancel with anything, right?
What are the flaws in my reasoning?