The soot would never be on the tubes themselves, since the flame stands above them, and the draft goes up. The first surface the soot particle hits is the heat exchanger.
When it's that sooted up it's worth cleaning it out, and it's far from the worst-case possible. If you can get a stiff bottle-brush to snake up in there you can usually get it clean enough- be sure to run a vacuum cleaner while you're doing it. You my have to pick at it with a sharper tool to get it started if the surface is getting hard-glazed.
Here's a video of somebody cleaning the soot out of a similar boiler.
Clean up all the burner tubes, and any obvious corrosion on the gas jets, then inspect for soot annually to see if this is a chronic mixture problem or if it was a one-off set of conditions that got it going.