There's a bit of dialogue in "A Piece of the Action" where Kirk states to Oxmyx that the Enterprise 'won't land,' implying that the Horizon actually did land on the planet and that the Iotians were not aware of transporters, which is borne out in the episode. This also implies that the Horizon did not have transporters, despite Starfleet ships in ENT having them. I got the impression, based solely on the context of APOTA, that the Horizon was a much smaller ship to be able to have landing and takeoff abilities, and definitely not a Daedalus class ship as was depicted in the Star Trek Chronology/Encyclopedia.
I have assumed similarly. And back in the day I experimented a lot with how the Daedalus-class might land, up to and including a separating "ball" section like Trade Federation ships in Star Wars! However, nothing in the dialogue discounts the use of shuttlecraft, so I see no reason to rule out the Daedalus. That said, I have always agreed that Sternbach's Horizon from SFC is excellent!
--Alex