In the case of small / short objects, the time it spends at the liquid-gas interface is, indeed, small.
However, I am also interested in the case of “big” objects, such as a really long cylinder (or missile, as in the case of your picture) where the time it spends at the interface is considerably longer, ignoring any rocket thrusters of course.
I can, as you suggest, simplify the problem by making a high-low estimate of what the drag force will be using the assumption that the object is still fully in, or out of, the water as it passes the interface.
As a physicists who rarely complicates things by taking into account drag, when I saw a discontinuity in my medium I thought, “hey, this might be an issue those engineers have to deal with sometimes”, but it would seem that it is me who is adding unnecessary complications.