It sounds to me like you will be using your Arduino in your home. That means that you aren't likely dealing with temperature extremes. That's one less thing to worry about.
How close are you planning to have your arduino to the tank? Humidity could be an issue if you're really close, well, close to exposed water. If you're a few feet away, you shouldn't have any problems there either.
1. A project box is probably the best way to enclose and protect your electronics. There are a number of different electrical connectors that you can use. Molex is readily available from Radio Shack. You can also get some inline headers or other connectors from places like Digi-Key. Probably not critical, unless you're using thermocouples.
2. This is going to be a matter of personal preference. Space inside the box will help you decide this also. You could use a terminal strip or a molex that "locks" into the hole.
3. I've never used one wire sensors, so I don't know how sensitive the communications wires are to other communication wires if they're in the same bundle. Might be good to consult the datasheets for the sensors on this one.
4. If you're planning only to run lights, you can have wire several feet long with no problems. When you get into situations where voltage is critical, you have to look at the number of Ohms per foot of a wire to help determine what gauge wire to use. This is in the hundreds of feet range. Not going to be a problem for you, I don't think.
5. Since you're going to have a very noisy environment, you will probably want to use a metal enclosure for your arduino. Be careful not to short anything inside it! Your sensor wires may need shielding. PWM for lighting shouldn't need any special consideration.
Hope this helps. I saw several reads and no replies. Happy building!