I would say no, because air is compressible and water is not. If pressure were equal then water would not pour in via vents and hatches etc. BUT, changes in air pressure is generally measured in milli-Pascals, i.e. tiny amounts.
milli-Pascals are potentially enough to make airs pop, but in the context of this discussion (forces to cause windows to suck in or pop out) I do agree that hydraulic shock is by far the more powerful force. In simple physical terms, with air, you have a weak easily compressible gas with which to transfer energy, with hydraulic shock, you have a solid, non-compressible water with substantial kinetic energy.
One proviso to add though, if you imagined a yacht being completely air and watertight, and being 2 m underwater, there is no way for the air pressure to equalise with the water pressure (assuming no way in for the water). In this scenario you are effectively turning the yacht into a submarine, and in physical terms in can be assumed to be a pressure vessel, with greater pressure on the outside. The structure of the yacht (windows) needs to be able to withstand that pressure differential. Its kind of getting into semantics now, as either way the windows need to be strong enough to not break when very big waves hit the boat...
My scenario was more the inverted boat being like a, let’s see, ... a teapot upside down. There are a number of holes that let water in from (now) below, until the air pressure inside = water pressure outside.