I'm skeptical as well as to starter calculators accuracy. Both Mr. Malty and Yeast Calc are done using the same set of experiments as a reference, and I don't know of any experiments comparing stir plates to shaking.
I would imagine that there are a number of other factors such as temperature and yeast strain that affect growth.
Here's a blog post on calculator accuracy:
And a proposed experiment:
If you want to know how many cells you have after the starter has completed, you can estimate it based on volume. It's also probably reasonable to assume that the viability in near 100%. If you are using DME to make your starter there is very little protein and you can assume 2 billion cells per ml. If it is from a mash it's more likely 1 billion cells per ml, but I have seen the vary from 250 million to 1.4 billion.
But if you really want to know, then like you said, you have to count them.
here's how I do it:
Instead of doing a starter, I like to reduce the amount of wort added at the first pitch.