Fully baked cookies in a 90 F car
Baked goods are generally considered to be a 'low risk' food when you're dealing with health codes.  That is to say, you don't typically need to worry if they've been kept in the 'food danger zone' for too long on a period.

In fact, I'd say that some of the best cookies I've had in the past decade were chocolate chip cookies that had spent an hour or two in a hot car shortly before eating.  (the chocolate was just to the point where it melted in your mouth as you ate it, without being so warm that it was melting all over your fingers).

So, is there increased risk?  Yes, especially if they had been contaminated with something before being put in the car.  But for breads and cookies, I wouldn't personally worry about a couple of hours at a warmer temperature.  

I'd be more cautious with baked goods more hospitable to microbial growth -- wet pie fillings, meat pies, etc.  Although pepperoni rolls are generally okay, as the pepperoni itself is something that's shelf stable for multiple weeks.  (and they're really good when they're slightly warmed, like having been in a warm car)

If you wanted to be really paranoid about the whole situation, you could've put most of the cookies in the fridge, but have left out a couple at room temperature in a sealed container.  This would serve like a petri dish to attempt to determine if there is significant microbial contamination to worry about.  If they don't go all strange on you after a couple of days, the ones in the fridge should be fine to eat.