If the amount of air in the bottle affects the quality of the EM and reduces it effectiveness. I've been told it does, and that its a good idea to siphon into smaller bottles as you drink it. I've only been having a teaspoonful a day so that would be very impractical! According to info I got from Vinny's website though, it doesn't really matter.
I store mine in a bottle (glass with plastic over the top, with a small hole....it hasn't exploded yet!) but it didnt fill to the top so there's lots of air space in there since I bottled it.
Ph has stayed the same...around the 3 mark so I assume its ok.