2004 Accord front brake question

I have a couple of questions about my V6 Accord coupe that baffle me.
My son was looking at the front brake pads through the spokes in the
front wheels and said that they looked like they were worn down and needed to be replaced. I agreed. So I pulled the wheel and the caliper off and pulled the pads and they were almost as good as new. Something about the way the caliper is engineered makes it so that you cannot visually check pad wear. This seems dumb. How do you know if the pads are in need of replacement? I can stand next to my Ford Taurus and see exactly how much pad is left.
Another question. Stupid me... when I went to remove the caliper, a began torqueig off the wrong bolts.. the ones most visible and with a rubber boot over part of them. They seemed to be able to turn in either direction and were very difficult turning them. Eventually I realized that I was turning the wrong bolts. But now I wonder if I screwed up some setting of some kind. I took the car for a ride down a steep hill and the brakes seem to work find. I jammed on them on a gravelly area and the anti-lock worked fine. What function do these 2 bolts serve?
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