I often pass through HNL on an international flight from Japan back to the US. I'm also a US citizen. You should be fine at immigration, as there will probably be more foreigners and their lines take more time.
As for baggage, not sure about Alaska, but I think that it's the same for all. After picking up your bag inside of customs (floor below immigration), you'll clear the final customs check. But, before going out the door, you'll be directed to the left to a place where international passengers in transit re-check their bags. You won't need to go to the regular ticket counter, as this is handled inside of the customs facility. That is, as long as it has a bag tag for your final destination.