When you check into a hotel and your name is not on the reservation the hotel most often (and is suppose to) change the reservation to your name (the party checking in).

So, once the room is in your name and you check out with a CC in your name, you can add your hhonors number to the reservation--before they ring you out (if you were the staying and paying party). Or, if you forget or do not add your number to the reservation, but it was placed in your name, you can call to have it added to your account. Because, if you are the staying and paying party it is your stay and you will/ can get your credit as an hhonors member.

That's simply how the hhonors program works. If the reservation was never placed in your name, you will have trouble getting credit and will likely not be successful in asking.