If you buy it from the App Store, it will remain available in your "Purchases" section to download later, even after Apple makes it no longer available for new purchase.
For example, OS X Lion is no longer available for purchase in the App Store, yet I can still download it, even though I'm running Yosemite! I also have iBank 4 available, even though it is no longer available, as iBank 5 has replaced it.
I would suggest going into your applications folder, select Aperture, right click and select "Compress 'Aperture.'"
I'm not sure if Aperture has any supporting files/folders that reside in other directories but if you want to try and see if it works properly, copy the compress file onto a hard drive or USB stick, log-into a guest account, pop the USB/Hard drive in and uncompress the app into your applications folder. Double click it and see what happens.
You can find another method to back up your AppStore content here:
(I don't claim to be a ditto expert, but I can tell you that worked for me. The -k option tells ditto to make zip archives. The --rsrc --extattr and --qtn options are all the default, so they don't need to be explicitly specified.)
I then copied the 'ReadNow.zip' file to my Dropbox so I would have it, just in case Apple removes the option to download it.
This should work for all Mac App Store apps (Xcode and "Install Lion" excepted), but may not work for other apps which use an installer and may install other files besides the ones in /Applications/.
Show me all of my Mac App Store apps
Speaking of the command line, if you want to see a list of all the Mac App Store apps that you have installed on your computer, you can run this command in Terminal.app:
Note: this won't show you Xcode, because Xcode is an unusual case. It is an installer which installs Xcode and then the installer is removed.
An ounce of prevention
There has been no indication that Apple will remove ReadNow from your list of Purchased apps, I just wanted to have a backup 'just in case.' Hopefully the "infringement letter" issue will be settled soon and it will be available again. However, if the iOS App Store is any indication, eventually jettisoned apps will become unavailable for re-download. Also, the upcoming sandboxing requirements may lead to some existing applications being removed.
As always, it's good to have your own backups rather than relying on being able to re-download anything from "the cloud." I wrote a small shell script which will look in /Applications/ for any applications which have the Mac App Store receipt, and create a .zip file for each of them. (While I have tested it myself and it works for me, YMMV, use only at your own risk, etc.)
To use it, download the script to your Desktop (or wherever) and then run:
chmod 755 ~/Desktop/backupmas.sh
And then run it via
(Obviously if you saved it somewhere else, use that path instead of ~/Desktop/.)
It may ask for your administrator password. If so, that's the one you use to log in to your computer, not your Mac App Store password.
The email I got doesn't mention "profile", it states:
"When Photos for OS X launches this autumn, Aperture will no longer be available for purchase from the Mac App Store. You can continue to use Aperture on OS X Yosemite, but you will not be able to buy additional copies of the app."
(my italics). So I read that you would be able to re-download from the App store, indeed given you have purchased it I don't think Apple is entitled to remove it.