I think it does matter, because it means certain behavior is more likely.
Companies that create patents are more likely to invest their time, money and effort into actually making things that will eventually be sold (in whatever fashion). This activity adds value to the economy. While it is possible for such companies to aggressively pursue their patents in the way that Lodsys has, they don't need to do it to survive, and I hope that the people who work there would rather spend time on more productive things. That's not a guarantee, of course.
Companies that merely collect patents, and exist solely to collect and profit off of the patents themselves, do not add value to the economy. They are parasites. Because they have no other way of generating revenue, we can expect them to behave in the way that Lodsys has.
If it was possible to design the IP laws so that patent trolling was not profitable, then I think that would be a good thing. I'm not sure if it's possible - but I think it's worthwhile to recognize that there is a relevant difference.