Calculating Kettle Salts

Using the post boil volume would be technically accurate in terms of finished ppm.

But using the starting volume is what software does and what most people mean when they give a ppm value.

 

Yes, assuming you're looking for a result close to what people are talking about when they share recommended ion levels.

 

3 g of Na (or anything) in 5 gallons would be about 159 ppm, but I think I know what you're asking.

Yes, if it's 159 ppm before the boil, it's going to be something higher than 159 ppm after the boil. The exact ppm would depend on how much you boil off. Let's say you start with 5 gallons of wort with 159 ppm chloride and boil it down to 4 gallons:

159 ppm x (5 gallons / 4 gallons) = ~199 ppm

But that doesn't mean you need to use less, unless you are targeting a specific ppm in the finished product. Again, when someone recommends, say, 100 ppm (or whatever) chloride for a sweet stout, they almost always mean the original concentration in the water, i.e. the water profile.

Just as an aside in case there are any pedantic chemists or engineers reading...
1 ppm <> 1 mg/L
But it's close enough at the concentrations we're talking about.