I delete them as I come across them. There is no benefit to keeping them, yet, in my experience, a number of problems have arisen with them in the past. I've seen the arrow incorrectly changed to disabled, naming issues and then there is the possibility of routing issues if the route hasn't been driven a significant amount of times. I think it ought to be best practice to delete them as you come across them, but, like erablian said, it's not worth while to spend a significant amount of time dedicated to tracking them down.
As far as adding junctions to increase penalties along a road, I've done this in very rare circumstances, essentially just on side residential streets that run parallel to a primary street. Often I find high road speed data is incorrectly given to these streets, resulting in bizarre detours down these streets. I'm sure there are a few more exceptions to creating extraneous junctions, but this is the only useful example that comes to mind at the moment.
If Anthony Henday has slow-downs at certain points during the day, the traffic data should be lower to reflect this. I don't feel that additional superfluous junctions should be necessary here, but that's just my opinion.