Mahou Shoujo Shinto Scion

[Valles]

Um, so if I'm reading that right, the ZOMBIE overheard what the characters were discussing  and got scared? So, the zombies here have capacity for rational thought and emotion? 

Sort of. Some forms of undead do - recall the skeleton that Yoko fought - but this particular one is animalistic. It just doesn't like loud noises, and started trying to get through the door to rip them apart until they quieted down again and it forgot.

This part seems to be missing bits? 'Rather than a more conventional' And I don't quite get the 'thought a bit more about 30cm from the hilt'. Was it meant to be something about drawing the blade out a little way to check it? Or is it a Japanese culture reference I've missed?

Sort of both. Properly, the passage should read:

And then she thought a little more about the deliberate notch thirty centimeters from the hilt, and blinked. “An homage to the Worochi-no-Aramasa?” she asked, fighting to think through the frisson of awe. That famous blade had been in the ancient tsurugi style, straight and double-edged, rather than the single-edged and slightly curved modern form that the nodachi was extended from.

In the myth about how Susano-o first acquired the Kusanagi, he's using Totsuka-no-Tsurugi to chop up the corpse of the monster Orochi, and finds Kusanagi buried in one of its tails the hard way, chipping Totsuka-no-Tsurugi. So that 'notch' was kept when the sword was reforged.

How does that translate into 'Oh - my mother who I know nothing about is the Goddess of the sun'? 
Earlier in the ep it was made clear that Yoko knew nothing about who her mother is aside from the stuff she got from occasional fatherly comments. Reiji's comments about the mother render down into 'Your mother had a Sunny personality' - which btw was a completely awesome foreshadowing. Maybe she extrapolated it from the boss zombie's comments - but it seems a stretch at least to me. Or am I missing a Japanese culture reference again?

Yatagarasu are crow-gods with three eyes and three legs, and are specifically known to be the chosen messengers and servants of the Sun Goddess, Amaterasu. Since this one has explicitly said he works for her mother, I don't think that there's a very big logical leap involved.

Their choice of MMPORG handles seem to indicate that although only Izuna 'knows' about their parentage, all of them are aware of it on sub-concious level?

And/or Fate is fucking with them.

Where are the other countries in all of this? Are they having their own issues? Does this mean we will see Scions of other Pantheons eventually?

They do have their own problems, which are fought by magical girls from their own national mythologies - for instance, King Arthur has reincarnated as a petite blonde teenager in Britain - but at this stage, their struggles aren't intended to be plot relevant and so will appear only in cameos and passing mentions.
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"V, did you do something foolish?"
"Yes, and it was glorious."