Without CO2 injection, there will be more CO2 in the water if you are getting a good gas exchange. There is CO2 in the air above the tank just like everywhere else and that will end up in the water. If you have the air pump at least a few cm above the water level of the tank, you need nothing to protect the air pump. If you have the air pump sitting next to the tank, like so many of us do, a one way valve is an excellent idea to prevent siphoning water when the pump goes off.
Yeah as mentioned above unless you are injecting CO2 in some form or another then better surface movement will increase the gas exchange and help get more CO2 into the water. If you do inject CO2 though then you want less gas exchange to stop the CO2 from going out of the water.
Nope, using an air pump to increase surface agitation with the aim of providing plants with more CO2 doesn't work I'm afraid.
A couple of years ago I was thinking about this in a chemistry lesson, came to the same conclusion as you two and was puzzled as to why people recommended that air pumps be avoided on planted tanks.
However, since testing my planted water for CO2 with and without the air pump turned on, and later reading Diana Walstad's 'Ecology of the Planted Aquarium' (excellent book, page 100 relates to what we're talking about here), I now think I understand why.
Sterile water in equilibrium with air contains 0.5 mg/l of CO2, but our aquariums (as well as natural ponds and rivers) contain considerably more CO2, for example my heavily stocked 50gal contains around 20 mg/l and my lightly stocked shrimp tank contains around 8 mg/l. I don't inject CO2 into either of these (yet). The CO2 is coming from everything living in the tank, fish, plants, snails and most importantly the bacteria breaking down the plentiful organic material in our tanks.
Increased surface agitation means more CO2 can gas off and the dissolved levels of CO2 will be closer to that of sterile water in equilibrium with air.
So I would suggest the OP stick to my suggestion of running the air pump during the night using a timer, if they want faster plant growth but still want the fish to benefit from an air pump.