Originally Posted by
beicster
It would have a very small effect on the chain if you are using a rear derailleur. If you are running it single speed, you could use them to set the chain tension.
It would probably be close, but the drop outs can get bent a little one way or the other. Also, if you want to make your wheelbase shorter, those bolts help you to get it exactly the same each time you put the wheel back on. As I mentioned above, I remove them. If I need to adjust the wheel to center it, I just do it by hand. Since I am not a racer changing flats mid race, I don't mind taking an extra minute.
Yes on both counts. On the last point, many bikes are ever so slightly out of alignment from the factory. A tiny discrepancy between the dropouts is magnified by the radius of the wheel. So even without a dropout getting tweaked, they're useful most of the time. I like to leave them in because it does make it easy to quickly center the wheel. Plus it just looks right to me, but then I also usually use a cap on the valve stem of my tubes.
EDIT: You also mentioned that the bolts don't seem to go all the way out. Most of the time, the are put in from the "front" of the dropout (the side towards the fork). Then they have a cap that screws onto the exposed end. Unscrew that cap, take the wheel out, and then unscrew the bolt so it moves towards the fork, and it should come out.