If I were you I'd start off by implementing a simple BSP (binary space partition) tree. Since you are working in 2D, bound box checks are really fast. You basically need three classes: CBspTree, CBspNode and CBspCut (not really needed)
- CBspTree has one root node instance of class CBspNode
- CBspNode has an instance of CBspCut
- CBspCut symbolize how you cut a set in two disjoint sets. This can neatly be solved by introducing polymorphism (e.g. CBspCutX or CBspCutY or some other cutting line). CBspCut also has two CBspNode
The interface towards the divided world will be through the tree class and it can be a really good idea to create one more layer on top of that, in case you would like to replace the BSP solution with e.g. a quad tree. Once you're getting the hang of it. But in my experience, a BSP will do just fine.
There are different strategies of how to store your items in the tree. What I mean by that is that you can choose to have e.g. some kind of container in each node that contains references to the objects occuping that area. This means though (as you are asking yourself) that large items will occupy many leaves, i.e. there will be many references to large objects and very small items will show up at single leaves.
In my experience this doesn't have that large impact. Of course it matters, but you'd have to do some testing to check if it's really an issue or not. You would be able to get around this by simply leaving those items at branched nodes in the tree, i.e. you will not store them on "leaf level". This means you will find those objects quick while traversing down the tree.
When it comes to your first question. If you only are going to use this subdivision for collision testing and nothing else, I suggest that things that can never collide never are inserted into the tree. A missile for example as you say, can't collide with another missile. Which would mean that you dont even have to store the missile in the tree.
However, you might want to use the bsp for other things as well, you didn't specify that but keep that in mind (for picking objects with e.g. the mouse). Otherwise I propose that you store everything in the bsp, and resolve the collision later on. Just ask the bsp of a list of objects in a certain area to get a limited set of possible collision candidates and perform the check after that (assuming objects know what they can collide with, or some other external mechanism).
If you want to speed up things, you also need to take care of merge and split, i.e. when things are removed from the tree, a lot of nodes will become empty or the number of items below some node level will decrease below some merge threshold. Then you want to merge two subtrees into one node containing all items. Splitting happens when you insert items into the world. So when the number of items exceed some splitting threshold you introduce a new cut, which splits the world in two. These merge and split thresholds should be two constants that you can use to tune the efficiency of the tree.
Merge and split are mainly used to keep the tree balanced and to make sure that it works as efficient as it can according to its specifications. This is really what you need to worry about. Moving things from one location and thus updating the tree is imo fast. But when it comes to merging and splitting it might become expensive if you do it too often.
This can be avoided by introducing some kind of lazy merge and split system, i.e. you have some kind of dirty flagging or modify count. Batch up all operations that can be batched, i.e. moving 10 objects and inserting 5 might be one batch. Once that batch of operations is finished, you check if the tree is dirty and then you do the needed merge and/or split operations.
Post some comments if you want me to explain further.
Cheers !
Edit
There are many things that can be optimized in the tree. But as you know, premature optimization is the root to all evil. So start off simple. For example, you might create some generic callback system that you can use while traversing the tree. This way you dont have to query the tree to get a list of objects that matched the bound box "question", instead you can just traverse down the tree and execute that call back each time you hit something. "If this bound box I'm providing intersects you, then execute this callback with these parameters"