1) Yes, there are always trade offs in evolution... cost/benefit analyses of a sort. So in the case of orifices, many have to do double (and triple) duty (depending on organism of course).

2) The combination of breathing/eating was pointed out as unintelligent design by Tyson because it is something that could easily be separated and would have functional survival value. All cetaceans have separated the two (because of their unique evolutionary history of being descendants of land mammals). You're of course right about the impracticality of "hearing through the nose".

3) Our digestive system is semi-efficient. It isn't necessarily weird that our digestive disposal system is where it is - but it is unfortunate that it has to be combined with our reproductive organs. That is definitely something that would ideally be separated, but meh, clearly it hasn't stopped me from engaging in the behaviour.

4) In terms of why organisms don't combine sight and hearing - I'm not sure it is connected to evolution of organisms in water. Eyes have evolved separately 20 times and not all of these independent evolutions occurred in an aquatic environment. I think it must have to do with the cellular complexity required for the two activities are very different, so it makes sense that those specialized cells require their own regions on an organisms body.