According to novelization (Disney canon), the reason for not knowing about twins - or even baby's sex - was that she wanted to be surprised:
“He?” Anakin asked mildly. “I thought you’d ordered your medical droid not to spoil the surprise.”
“Oh, I didn’t get this from the Emdee. It’s my …” Her smile went softly sly. “… motherly intuition.”
He felt a sudden pulse against his palm and laughed. “Motherly intuition, huh? With a kick that hard? Definitely a girl.”
(ROTS novelization by Matthew Stover, Chapter 12, "Not from a Jedi")
Please note that this is quite a normal thing in earth medical practice even today, when we have ultrasound. Tons of people I know chose not to find out. I assume medical doctors on Earth would at least say something about the twins for medical-risk reasons, but then again he's a human being, NOT a "medical droid" who can be ordered to shut up.
Apparently, she never did find out and kept it a surprise:
“If it’s a girl …,” she gasped, “name her Leia …”
One of the surgical droids circled out from behind the tent, cradling in its padded arms a tiny infant, already swabbed clean and breathing, but without even the hint of tears.
The droid announced softly, “It’s a boy.”
Padmé reached for him with her trembling free hand, but she had no strength to take him; she could only touch her fingers to the baby’s forehead.
She smiled weakly. “Luke …”
(ROTS novelization by Matthew Stover, Chapter 21, "A New Jedi Order")
Disney Junior Novelization of ROTS by Patricia C. Wrede is even more explicit in that she did NOT even consult a medical droid in the first place:
Padmé laughed. “He keeps kicking.”
“He?” Anakin’s eyes widened. “Why do you think it’s a boy?”
“My motherly intuition,” Padmé teased. Even if she’d consulted a medical droid, she wouldn’t have asked. Wondering whether she carried a boy or a girl had been one of the few, secret pleasures she had during the long months Anakin had been away.