If their patent work left them confident that there were OK, then the courts will see if they're right. If they chose to take a chance... this is what can happen.
The only trouble with that statement is that it's completely incoherent. On the most charitable reading of it, there is no way not to "take a chance." This is, in fact, the very thing that you're obscuring, whether by accident or design. If the patent system is a structural quagmire that stifles innovation, then that is the problem precisely because "due diligence" is impossible.
Incredibly, you continue:
But Nest is no victim here...
Yes. Yes, they are. They may be an affluent victim. An able victim. But a victim nonetheless. And, as long as this kind of victimization is allowed to continue, innovation will continue to carry a market-altering penalty that retards human progress. And, lest you think I'm being grandiose in my assessment of this thermostat as an example of human progress, it saves energy, and energy is one of the more pressing problems facing humanity.
They knew what they were getting into.
"But, ladies and gentlemen of the jury, look at how short that skirt was, and she decided to walk home on a Friday night! Drunk! Who's the real victim here? My client couldn't resist!"
... who, as the GP points out, played the game with the best of them. Live by the patent sword, die by the patent sword.
I like the idea someone posted on HN a few months ago; it should be possible to "opt out" of the patent system entirely. You can't be sued for patent infringement, but you also can't hold any patents yourself. Let's do that, and watch the market determine whether patents are really good for innovation or not.
So if Nest had owned no patents, Honeywell would not have sued them? I find this exceedingly hard to believe.
This is a stupid idea.
Basically, anyone who does actually invent something that's legitimately worth patenting (by whatever metric you please), then patents it and (as required by the process of patenting) details the invention, somebody can just come along and take that work and use it and the inventor gets screwed.
Fix the patent system or ditch it. The opt-out idea, though, is nonsensical.