Yes and no - I've had Applications (Parallels) in my privacy tab for years, since a previous Parallels version on a previous machine (I did a TM restore onto my MBA last year). I've looked through Alfred's options a few times to try hiding the windows apps, both v1 and v2, but only last night did it bug me enough to start googling for a solution.
Anyway.
Before I posted I tried removing the folder from privacy, waited a few seconds and then re-added it. Now something weird is going on; I removed the folder and windows apps don't show up!
They're not in either Alfred's results or the Spotlight search (but they do in Spotlight "show all in finder" search). One of the things I tried last night was turning off Parallels sharing windows apps with the mac, but I turned it back on after a few minutes.
My MBA has been asleep overnight, maybe it woke up and did some maintenance that changed something... Admittedly I didn't check if they showed up this morning before removing it.
I'm confused, but happy they're gone from my results. I'll post back if they mysteriously return.