As for the years passing, I'm pretty sure I read in one of the ZUN interviews or something that "the gensokyo timeline isn't really connected to the real world or anything. There might be several incidents during one year". But he's always been deliberately vague about everything like that. But that was also a long time ago. I don't think he actually wants to take the main characters out of their teens, though.
For my stories, I usually count them in real-time though, that is, one larger, world-breaking incident (the game incidents) per year, roughly. If the heroines were 12-13 in EoSD, that would make them around 20 in SA, and around 25-26 now. I'm pretty sure they're considered younger in ZUN's own version, though.
The dialogue referenced is 90% surely just cheeky banter, as always.