Yes, you are allowed to have many inlet and outlets applied within your setup. Example setups tend toward simplicity in order to teach/illustrate a particular point and so they do not tend to have dozens of inlets/outlets. It is possible for you to do that tough, if you wish.
The problem with making this an internal analysis is that you would not reasonably be able to apply just environmental pressure to all the inlets/outlets. Some of them have to be flow conditions in order to get the air moving. You would need to know fairly exact flow speeds for your inlets to facilitate this (this is somewhat unreasonable to expect to have on-hand. You may wish to switch your analysis over to an external study which leaves all these holes (inlets/outlets) open, without lids, and apply an external flow across the model to represent the wind passing around/through the structure. In this way, the program is solving for how much air is flowing in/out of all the openings.
Your incorporation of a free surface of water is your real problem though. Flow Simulation cannot handle free/open surfaces of liquid in the same chamber as a gas. For that, there is no workaround really so your analysis may need to be done without that included.