So I am pretty I am the person that Stickzula was referring to - and so you defintely want to put a sealer on the inside as well as the outside. I think its also a good idea to use a mildew resistant paint primer on the inside. I have read several posts of people getting mold on the inside of their hood. My hood is actually very similar to your design except I do not have the break in the top - the whole top of my hood lifts up. I used lift supports instead of hinges. Theoretically they keep the top up when it is opened so it doesnt fall back down. However, there are basically two different kinds of lift supports - cheap and really expensive. I bought some cheap crappy ones so you really have to push it all the way back to make sure its locked in. So I would spend some time looking into that. Originally I wanted to use gas springs (the kind that lift the trunk if you car) because I think that would be so cool, but apparently they are really complicated.
Also, think about whether you want the top of the hood to sit inside the sides or to side on top of the sides. There are pros and cons to either approach.
I would also not make it too high I think aesthetically and practically thinner is better. Most hoods are made very high (I think by high I mean deep) because they open in the conventional way - where the front half of the hood both the top and the sides lift up. So you need to be able to get to the water when the lights are installed. However since your lifts lift up with the top of the hood you don't have that problem. So as far as the height goes you only need to make it deep enough to include the amount that overhangs the tank + the height of the lights + some margin. This "advantage" is why I went with this design. Also the more height you give the hood, the taller you need to be to reach in to the access the tank (this is the disadvantage to this design).
Lastly, if you are going to use molding on the corners of the hood, going with two sepeate pieces to make the top of the hood means you will have to have a break in the moulding on the top - so one can be open when the other isnt. This is one thing I regret about my hood - and I wish I made the top one whole pieces. However, then it becomes a little heavy, especially if you are using 3/4" wood. I am actually trying to think if there is some kind of cheap solid plastic I can use to replace what I currently have, which is two 1/2" pieces of plywood. Plastic would be more water proof and lighter.
Anyway, a few things to think about.