Well, I disagree-- I think that all of the votes should be counted regardless of whether it will change the outcome in a given state or not. Besides, there are a lot more races on the ballot than just the Presidential race-- if they don't count the ballot, how do they know that the outcome of some OTHER race might not be different? That's some pretty fancy decision-making, it's easier just to count the damn votes and get the totals right on all races.
They do count the votes if they could change the outcome in any race. But most of the states that ignore votes are pretty partisan one way or the other (usually Dem).
Counting absentee ballots is pretty expensive. I don't favor spending millions of dollars to find out that a candidate won by 500,000 votes instead of 505,000 votes.