Tomos
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I see the same problem, but I think I might have an answer that makes sense.
Taking 10 on checks in book one of S&S seems to be somewhat of a contentious issue. See this thread for a discussion. It's not specifically disallowed by the rules, but it seems to be likely to ruin the fun of it.
By RAW, Taking 10 may not be allowable with the Sneak option as there is (conceivably) immediate danger or distraction. When Sneaking, the PC would be a bit rushed, since they spent enough time to do their job right during the day. Being discovered and accused of stealing could be very dangerous to a PC.
Shirk seems to represent taking plenty of time to be careful while poking around the ship since the PC is really not putting much effort into their work (-2 penalty). They're spending the extra time to make sure they are not in immediate danger.
That's probably how I will handle it.