There are two accounts under my control. If I merge them into one (I saw the concept of merging in a previous meta post) will my reputations on both be added up to one?
Yes, the reputation earned on both accounts will be added.
An exception is reputation generated by interaction of the two accounts. If one earned for example some reputation points on one account from having a suggested edit on a post by the other accepted, that reputation will be nullified. And of course, hypothetically, if there are votes from one account on posts of the other account, such votes would be invalidated when accounts are merged.