Ignoring the classic joke that says you look out through the screen door, there are a number of ways of "seeing" outside.
Some submarines (especially small submersibles, research subs, and "tourist subs") do have glass windows.
Most submarines do not. They use other means.
A. On the surface, they have periscope (either direct sight or fiber optic). They have navigational radar. They have direct vision from the bridge of the sub (if it is fully surfaced and not simply at periscope depth).
B. Underwater, they have active sonar and passive sonar. Active sonar is like what bats use to echo locate what is in front of them. Passive Sonar is like using sound to figure out what is coming your way (like using your ears to safely walk around town with your eyes covered). Another primary method is Inertial Navigation. Using inertial navigation equipment tells you how fast you are going and in what direction. As long as you know where you start from, combined with good ocean charts, you know what is in front of you, above you, below you, behind you, and on each side of you. Fathometers (a lot like active sonar) can tell you how far you are above the bottom of the ocean, while pitot tubes can tell you how fast you are moving and how deep you are.
Combining all of these different sensors can be quite powerful. Much more powerful than looking out through a big glass window... you would not be able to see very much anyway.
Team Magma will not appear in the submarine but you will see them get away with it the first time. The second time you see the submarine, you have to dive to the seafloor cavern to go challenge Maxie.
A submarine.
An RC Submarine is a submarine purchased at a toy or hobby store that is run by remote control. If you want to see a sample of an RC Submarine you can find one here: http://www.amazon.com/Swimline-RC-Submarine-27-MHz/dp/B0037M4Q3A
See flying Tiger Submarine Launching Tags, anywhere from $28 to $400
Other than the periscope, which was designed to be extended up above the surface of the water to see what's on top, there isn't really a way to look out of a naval submarine. There are no windows or the like.
See website: Submarine
See Sources and related links.
A periscope is the instrument used in a submarine to see above the surface of water. It works by using mirrors to reflect light down into the submarine while allowing for observation of the surface without exposing the submarine itself.
They use a periscope. See the related link for more information.
The captain of the submarine raised the periscope to see if there's danger.
Go to the submarine and press B. You'll notice you can get up there. If you are above, you'll need to explore a cave with team aqua in it.
Prior to radar, you couldn't hit what you couldn't see.