I am having an AEM v2 installed in my '06 S. It seems to me that the air guide plate (#2 in the picture below) will no longer be functional since I am removing the stock air box (and not replacing it with a similar air box (i.e., Mugen, J's Racing, etc.)). Is it safe to assume that I can remove this piece?

 

Keep it on. It helps to direct air into the condenser/radiator.

 

Really? I haven't spent a lot of time looking at the design (in person), but it seems to me that this guide may actually pull some air away from the radiator???

 

Look again. If you'll notice, Honda put slits into that guide so air can get past it and go up and supply air for the stock airbox. If not for the slits, most of the air would go through the radiator.
Of course, it depends on where you live and drive your car. If you lived in a very hot environment, you'll need all the air you can get going through the rad, not going up and over the the rad.
It's not like you're putting in a snorkel where the airguide has to be dealt with. Why remove something that was put there for a reason? If I operated the car in a really hot place and put on an AEM, I'd use black duct tape to close up those slits and maximize the airflow through the rad.

 

I live in San Diego. Gets pretty warm, but not extremely hot. I have a thing about removing parts that lose their intended functionality. If I went through the trouble of taping the slits on the guide, I might as well remove the darn thing because it is just wasting space.

 

Well, it's your car. Give it a try and keep track of your coolant temp readings.
Taping up the slits increases the amount of air going through the rad (better cooling). Removing the airguide will dramatically decrease the air going through the rad (inefficient cooling). Your choice.

 

Leave the air guide on. It weighs only a few ounces, and serves a good purpose of directing air though the radiator.

Removing it will let more turbulent air under the hood.