Add to this that Khan thought he was stranding Kirk in the center of a dead planet. Emphasis on dead. He hadn't been to the Genesis Cave. Khan's men never got any further than the station. He didn't know there was a natural paradise waiting for Kirk's landing party. He'd have been as amazed as Kirk was at what they found there.
But if he scanned the planet to locate the Genesis Device, wouldn't he have noticed all the flora down inside a dead world? Any other time, sensors can locate a pimple on an ant's ass but here completely miss a giant cave full of plant life and water?
It really is no more complicated than they wrote themselves into a corner so they changed Khan's motivation. It works because Shatner and Montalban chew enough scenery that you get lost in the performances.
What's he scanning for?
It's pretty clear that his interest isn't solely one of revenge. As soon as he hears about Genesis, he wants to know more. "I agree to your terms. If ... IF! In addition to yourself you hand over all data and materials regarding the project called ... Genesis." He's tricked Kirk into stranding himself in the center of a dead planet. He's got his revenge, now he wants Genesis. Captain Terrell has given
Khan the location of the Genesis device itself, so Khan and his people don't even have to scan any further than to operate the transporter. Terrell and Chekov were Khan's eyes and ears prior to that and he knew as much as Kirk did and likely came to the same conclusions. "I thought this was Genesis?"
Under all that rock, it was a miracle the transporters worked ... It's even easier to conceive of a skeleton crew of refugees from the 20th century lacking the competence required to notice the life-filled bubble scores of meters away from the center of attention.