This isn't a dumb question, especially given the change in seasons.
Extreme temps (hot or cold) aren't good for leather skates at all. The heat triggers re-molding and the cold freeze-dries the leather. I used to take my skates into my office if I needed to coach after work but we didn't have metal detectors. In your case, I think I'd leave the bag in the car and just hand-carry the skates. Go to the same security guard if you can, so you don't have to explain why you have ice skates in the middle of July.
If you really, really have to keep your skates in the trunk, do it with some precautions: put the skates inside a soft-sided cooler in the trunk. You can pick one up really cheap at a thrift store. In the heat of the summer, put a frozen blue-ice pack in the bag each morning to offset the high temps. For cold winters, I guess you could use a microwave-gel seat. Nuke it and put it in the cooler.
http://www.amazon.com/Lava-Buns-Heated-Seat-Cushion/dp/B000KU74MMThe problem with the frozen boots is that the cold transfers to your feet when you use them as skate warmers, lol. You can use a hand/hairdryer to take off some of the chill. Some people put the boots under their car's heater vent, others use their heated seats feature, lol.
In the winter, I use sk8dreams' rice skate warmers. Really easy to make: take a thin sock, fill it partway with ordinary rice, tie a knot in the end. Microwave for 1 minute, then put inside the boot. It doesn't get hot enough to trigger any heat molding and the boots are nice and warm to wear on a cold 5am freestyle. (Put the rice sock in your sneakers while you skate - it's a nice treat après-skate!)