Try applying the translation patch to it (make sure you use v1 though, v2 of the translation causes problems with the pokedex). I don't think v1 is available on the original site anymore, so I'll attach it here.
I used VBA 1.7.2, applied the patch before playing, and had no problems.
Pokemon Emerald does not have the Day/Night effect, though the internal clock is running normally (go to your house and look at the clock inside your bedroom, you can see what time is it by looking it).
If I can remember correctly, neither Ruby/Sapphire and Emerald versions have that effect. The only thing I think that is based in clock-event is the tide of shoal cave. And that damn Mirage Island.
Resuming: your game is normal and you don't need to worry.