Yeah, but I also think you're correct in that if the Z-probing hits the pads, then it probably takes those into account. So this might not be the issue I thought it was.
I've been playing with some new ink (haven't tried the solder yet), and I'm still going through nozzles like candy. This time around I don't think it was the pads, instead I broke two nozzles in a row due to some other sort of error in probing. The difference this time was that since I was going to actually bake, I had my mill pre-drill the holes and vias. (request for feature: a Pi Hat template that doesn't have the corner holes, since it just wastes time on my mill)
So what happened this time was that the ink cart started a trace that began at a through-hole, and the edge of that hole was higher than the probing accounted for. So the nozzle dove deep enough to clip the edge of the hole, bending it badly, and that was that.
When I backed things up enough to re-align/re-probe the board, the Z-probe also dived into the hole just enough to gouge across the board and then the software threw an error. That happened twice in a row (odd it didn't happen the first time), I then thought to pull the clamps further away so they were closer to the edges of the board. Since this was the 2nd side, I think I was getting some flex from clamping that the probing wasn't accounting for. At any rate, that allowed the probe to succeed, which allowed the ink to lay down without eating yet another nozzle, and now both sides are baked.
Then it was on to after-school kid duty.
I gotta say that the cost of the nozzles are adding up. They bend/break just by looking at them funny. I know that they are inherently fragile, but it would be nice if you could get the manufacturing costs down somehow so that it's not so painful on this end every time one breaks or clogs, which happens all too frequently.