The script directions make that abundantly clear that she did notice his extra heartbeat but didn't really know what to make of it.
MARTHA : Sorry, um. Right... Right...
She puts the stethoscope to left of his chest. Ba-boom-baboom-ba-boom.
But under that, an echo..? She looks up at the Doctor, puzzled. He
just gives a big smile.
She moves the stethoscope over, to his right side. A second heartbeat,
Martha looks up, astonished, right into the Doctor's eyes. And he
gives her the smallest wink.
Later on when he tells her that he isn't not human, she still doesn't believe it
He's just rising up, cautiously, stepping out - on Martha,
following, a beat behind -
MARTHA : Oh I like that, 'Humans'! I'm still not convinced you're an alien -
Right in front of THREE JUDOON. The lead Judoon holds up his device,
shines a light on the Doctor's forehead.
Wip-wip-wip - but then - wreeeeeeeeeeeeeeee!
JUDOON : Non Human!
MARTHA : Oh my God, you really are!