It means they cannot be found again unless you saved before you fought them then you can just restart. If you saved after you killed them then you can't find them again, so you have to restart the game if you want to catch them.
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You get a diploma in each, in emerald you can get a johto starter from prof birch and that's it.
No you can water them infinite times and nothing bad will happen.
Emerald City Confidential happened in 2009.
The Internal Battery has most likely died. This Can Happen to any cartridge over a long period of time.
Cyndaquil and all other pre-fourth generation starters are unavailable in Pokemon pearl and diamond. You must transfer it from Pokemon Emerald. If you do not have Emerald, sign up on a Pokemon trading forum and find someone who is willing to trade you one.