My Pokemon Sapphire finally came but it says that the internal battery has run dry and clock based events will no longer happen or something like that...what does that mean and what's gonna happen?
It doesnt really affect the game. The game battery that runs the internal clock has just died. Any time-based events (i.e. berry growth) or things that happen once a day (i.e lottery) will either stop or will be locked into one option (eeveelutions).
Your game itself is still fine.
Source: experience and here