I'm with Scooper. As long as a sufficient amount of weld is left in place the weld should be fine. Creating a uniform surface should create a more uniform stress load. Where one could run into a problem is filing a weld down to it's lowest point and that lowest point actually being too low... i.e. welder error.

I'll not bring the 'art' argument in as I think welding well is incredibly difficult. In shop class I could lay awesome arc welding beads but I know I can't even begin to MIG or TIG. It's a craft, no doubt about it. While the outcome might not be aesthetically pleasing to all.... it's still an art form.