I will try one more time to say the same thing that has been said before hoping that this time it will stick. Your original question was "How to use Newton's second law to treat differently the two cases below in which a system has its mass increased?" If I look at the "two cases below", I see no system that has its mass increased. Specifically in case 2 all I see is a drop with zero horizontal velocity and a cart with some water in it moving with horizontal velocity ##V##. This is the "before" picture. In the "after" picture you have the drop added t the water in the cart and the ensemble moving with common velocity ##V_{\text{after}}.##
Now, there could be 3 choices of system here:
- The drop that has mass ##m_{\text{drop}}##
- The cart with the water before the drop falls into it that has mass ##m_{\text{cart}}##
- The cart + the drop that has mass ##m_{\text{cart}}+m_{\text{drop}}.##
Before you apply Newton's second law, you have to declare clearly and unambiguously your choice of system. If I look at the choices above, I see no system that has its mass changed. There is momentum transfer between the drop and the cart. In order to apply Newton's 2nd law in this case, you must have a consistent choice of system throughout the momentum transfer process.
To put it bluntly, if you say that you choose system 2 (cart) before the drop falls into it and system 3 (cart + drop) after the drop falls into it, you cannot expect to use Newton's 2nd law to say anything meaningful. Changing systems midway through the calculation is analogous to changing the origin of coordinates midway through a derivation of equations of motion.
Here is how one would apply Newton's laws to case 2.
The system is drop + cart
The external horizontal force acting on the system is ##~F_{\text{net,x}}=0.## The momentum of the system is $$P_{\text{sys,x}}=m_{\text{drop}}*v_{\text{drop}}+m_{\text{cart}}*v_{\text{cart}}.$$Applying ##~\dfrac{dP_{\text{sys,x}}}{dt}=F_{\text{net,x}}~##, $$0=\Delta P_{\text{sys,x}}=m_{\text{drop}}*\Delta v_{\text{drop}}+m_{\text{cart}}*\Delta v_{\text{cart}}.$$ The last expression gives the final velocity of the system $$V_{\text{drop+cart}}=\frac{m_{\text{cart}}V}{m_{\text{cart}}+m_{\text{drop}}}.$$
The system is one of cart or drop
As noted above there is no external horizontal force acting on the system of both the drop and the cart. This means that $$0=\frac{dP_{\text{(cart+drop)}}}{dt}=\frac{dP_{\text{cart}}}{dt}+\frac{dP_{\text{drop}}}{dt}\implies m_{\text{cart}}\frac{dv_{\text{cart}}}{dt}=-m_{\text{drop}}\frac{dv_{\text{drop}}}{dt}$$ This says
(a) if the drop is the system, the net horizontal force acting on it is ##F_{\text{on drop}}=m_{\text{cart}}\dfrac{dv_{\text{cart}}}{dt}.##
(b) if the cart is the system, the net horizontal force acting on it is ##F_{\text{on cart}}=-m_{\text{drop}}\dfrac{dv_{\text{drop}}}{dt}.##
Note that the net horizontal external forces acting on each system are Newton'w 3rd law counterparts.