There is no immediate effect on Pear Note. The current version of Pear Note will keep working just as it has outside the sandbox. Apple is only enforcing this rule on new apps and updates to existing apps. So, I can't submit an update to the Mac App Store that is not sandboxed. Well, actually they've made an exception for "bug fix only" updates, but I can't add features without sandboxing Pear Note.
As I said in my comment on Andy's blog, Pear Note should fit in the sandbox without problems. Unfortunately, there are pieces of Mac OS X itself that don't behave properly within the sandbox, and Pear Note relies on one of these. Until Apple fixes this, provides a way around it, or I come up with some other way of doing things, I can't sandbox Pear Note. So, I can't update the Mac App Store version of Pear Note.
The good news is that 3.0 just came out, and I have no immediate plans for a feature update right now (I'm focusing on the iPhone version right now). So, hopefully Apple will fix their bugs and Pear Note will become sandboxed without issue. I'm fairly confident that this will be what happens.
The absolute worst case scenario would be that Apple doesn't fix things or provide an alternative mechanism and I cannot find any way around the problem. Even in that case, Pear Note will continue on outside the App Store and I'd find some way to gracefully transition App Store customers to direct customers. I think this is a very unlikely scenario, but it's the scenario that's got me worked up and complaining.
So, don't worry about Pear Note. There are a lot of apps that can't work within the current sandbox by design, and those apps have it far worse. Pear Note will work just fine as soon as Apple fixes some of its own bugs. I had just hoped they would fix them before they started forcing App Store updates to use the sandbox.