- Yes, operator is a little slower, especially if you have exceptions/etc turned on; it checks whether range is valid, etc. However your loop isn't big enough to make a any noticeable difference.
- std::clock() has horrible accuracy. Even if there is performance difference you won't notice until it's huge or it'll round wrong way giving invalid data, ex. execution time can increase by 1% by rounding will change from 16ms to 32ms. Pointers aren't "faster" or "slower", however when misused they definitely can be slower because of cache misses.
- I have suspicions that your handConflictsBoard() function passes values instead of references, thus copying a lot of data when it's not necessary which is likely source of your slowdown.
If you want to make your code faster first you need to figure which part is the slowest and then see how you can improve it. Optimizing random code parts isn't likely to give significant difference.