If you are not expected to pay a bill for the room (just for incidentals) then it is very likely to be a specific conference rate and therefore, as others have said, may be negotiated to exclude any HHonors benefits or to have those accrue back to the company doing the booking. That may also explain why the listed price is higher than an on-line rate, for hotels sometimes charge a premium for block bookings as they are taking a risk on large numbers of rooms being booked and then cancelled at a short notice.

We often use our clients' corporate codes when booking hotels (as they are cheaper than our corporate rate) and have always paid at checkout and received HHonors points appropriate to the rate.