Without wanting to sound too disheartening, I wouldn't worry about this kind of stuff for the time being. Concentrate on writing solid code and understanding the language (for instance, free store vs automatic storage semantics is particularly important point in a value-based language such as C++).
I was actually trying to generate cache misses with this code. I have read all about them and would like to experience them for myself.
If you really care about how much you're missing the cache, it's not something you want to be working out in your head, for the most part. You first want to write code sensibly and then use profiling tools to tell you where you might be able to improve it in terms of performance. Intel's PCM will give you really low-level information of this kind.
Neither. Typically use reference-to-const for non-primitive types. Tweak according to profile results. Again, IMHO getting the basics of the language down first is much more worth while.
I wanted to know if it was better to send in a pointer to a structure for a often called piece of code,
Whether or not an object is on the stack or heap makes a difference, as does its size, and the amount of indirection inherent in its data structure. The full answer is extremely complicated.
or to just pass the structure by value to avoid a potential cache miss.
If you insist on learning more about this stuff (and again, I don't think it's necessarily a good idea at this point in your education), a good starting point is this article which demonstrates cache effects on performance. Note how the expert himself failed to explain all the effects revealed by the data. You could try replicating the results yourself in C++:
I might not be getting cache misses because I have a 15MB L2(3?) cache, but I know not all systems have that.