Good point.
It's no indication, but it would generate fear and doubt when I code. What if the code I'm writing right now is patented by some company taking advantage of a system, with resources searching everywhere just to sue? I probably wouldn't, but I could become paranoiac because of this, looking on the internet to find if I am infringing patents, instead of being productive.
It's true 1.36% seems like nothing, but for a small company, it could mean a lot. Plus, it would be heart-breaking (or even outraging) to know that a program I made on my own, with no knowledge about some software patent, nor ill intention, gives money to someone that has nothing to do with it.
And, as you mention, legal costs, time wasted and stress could easily be real threats to a startup.