The clock has NOTHING to do with the internal DS clock or anything like that.
The clock in pokemon games is regulated by the internal battery. If the battery goes dry, then the internal clock stops working. It's not set by anything in any internal system, but by the user at the beginning of the game.
As for emulators, you just have to set the emulator properly.
Go to Options -> Emulator and check Real Time Clock.
Eh...Unless they put internal batter clocks in the ez 3 in 1...the idea of having RTC in the game isn't happening -.-
Just play on the gameboy advance emulator on your computer. (there's an option that turns on the RTC for the GBA emulator; not the expansion pack)