[susan53]

Yes - it's the same difference as in :

a) Who did John phone?
John phoned Mary.
Do you know who John phoned?
and
b)Who phoned John?
David phoned John.
Do you know who phoned John?

As the underlining in the examples show, when the question word is/refers to the object or complement - as in (a) then the question uses inversion. But in an indirect question this is lost and the order becomes Question word - subject - verb : ... who John phoned.

But when the question word is the subject, then there's nothing else to put in front of the verb, so in both the direct and indirect question you get question word (=subject) - verb - object : ... who phoned John.

So in your examples
a) Where is the nearest station?
The nearest station is over there.
Where refers to the complement so -
question = inversion :Qu word - V - S (Where is the station?)
indirect question loses inversion : Qu word - S -V (...where the station is)

But :

What percent of Japanese are Christians?
2% of Japanese are Christians.

The question phrase (underlined) = subject. So there's no inversion in either the question or indirect question - it's always question phrase - V - S