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In RotS, the "shields are still up" are in reference to the main defensive shields.
I don't think so, the narrative continuity is pretty direct (I'm watching the sequence as I type,
"Well, have you noticed that the shields are still up?!"
"Sorry, Master..."
Anakin blasts gadgets right by the door, the blue lights splutter and go out, atmosphere starts rushing out, and the emergency blast doors close.
In cinematic terms this is fairly simple - the shields Obi-Wan refers to are the shields that Anakin disables, so the ones that retain atmosphere in the hangar. The fact that these shields are a problem for the two Jedi Fighters would indicate that these shields either both retain atmosphere and screw up ships entering, or there are two kinds of shield at the same time, but certainly, we're talking about the hangar shields, not the primary shields.
As an aside, it seems to me that starship shields, on the order of capital ships, are set a surprisingly long way from the hull - capital ship combat seems to take place mainly within the perimeter, with cannonades simply pounding the bejesus out of each other's armour. This may well be why the Death Star's field is so far out...
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If something goes wrong and you need a biological maintenance member, or to greet incoming ambassadors or Jedi, it would be too time consuming to bring up an appropriate environment every time that the ship came or went.
That that is the sort of opinion that needs backing up - what figures are you using to estimate repressurisation?
In anycase, if we're talking about, for example, Lucrehulk ships, then we know there's a command orb in the middle, and cargo arms forming the bulk of the ship. I think it wouldn't be at all unreasonable to assume that under most circumstances the arms are not pressurised. Normally biological visitors would go directly to the Core Ship. The DCS that recieves the Jedi Delegation could well have pressurized a section to accomodate the Radiant VII, which may have been too large to dock with the Core ship itself.