I'm not sure how you are doing your math. Intelligence does not affect damage, it does increase the DC of the save.
And since a successful save means half damage, Intelligence does in fact affect damage.
Assuming a 5th level Wizard with 16 intelligence, the DC of the save is going to be 16. A Kobold with a +1 Reflex save needs to roll a 15 or higher to make the save, which means they will make it 30% of the time.
Correct...
Assuming an average damage roll of about 16...
Whoa, stop right there. You don't get an "average damage roll." You get a damage roll, which can have results from 5 to 30, or 2 to 15 on a successful save. Those results are distributed on a bell curve. The kobold's place on the left side of that bell curve determines its odds of making it through.
I actually plotted this out with an Excel sheet (a computer is really handy for this kind of thing; instead of calculating probabilities by hand, you can just brute-force it and compute every possible result). Without getting into all the details, what it boils down to is that a failed save is essentially a death sentence. Even the toughest kobold, with the full 8 hit points, has only about a 1 in 370 chance of survival if it fails its save.
The saving throw is how tough kobolds survive. The odds of rolling 7 or less on 5d6 are miniscule, but the odds of rolling 15 or less are pretty decent--a bit over 30%. If the kobold makes the save, its chances are still nothing to write home about, but they're well above zero. So the wizard's Intelligence, by changing the odds of making the save, has a big impact on kobold survival rates.
But also, in 3e, the kobolds don't actually die until they are at -10, and in Pathfinder it is negative Constitution. A Pathfinder Kobold has 5 hps (unless you roll then it is 1d10), and an average 10 Con. So, a fireball has to deal 15 points of damage to kill them outright. In 3.5 it would be 14 hp's. If the kobolds have a cleric with them, capable of channeling energy, the average fireball may knock most of them out, and may even kill about 70% of them, but the ones that make their save are by no means out of the fight.
I'd have to go back and check to be sure, but my recollection is that according to the 3E DMG, death at zero is standard for monsters and NPCs. The negative hit point rule is meant for PCs, although the DM has the option to apply it to monsters if s/he wishes.
If the kobolds had a cleric along I might take that option, but generally I assume a monster that hits zero hit points is out of the fight and effectively dead. If players want to check for survivors and take prisoners after the battle, I'll make up something on the fly and roll to see if any kobolds are still breathing.
