I have the retail version. I have iLife on a disk too, but I have not installed it.
The iWork"09 folder has always stayed in the application folder.
I am NOT aware of anything I have removed from the system.
I have run Disk Utility before and ran across something which it said could not be repaired. I just did it again and got the samead also updated my software just a few days ago. There were a ton of permissions in iTunes which needed repaired and a few in Safari but that was it. Nothing for iWorks applications. I had also updated my software just a few days ago. Here is the info regarding what could not be repaired:
Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent” has been modified and will not be repaired.
I have NOT had any issues with any other programs.
I just opened pages again and though it comes up all I get is the template chooser and then the chooser screen is solid black.
Keynote says an unexpected error occurred - pleas quit Keynote. But I have to force quit to get it to close.
Numbers does the same thing as Pages with the template chooser.
(For having Macs for more than 20 years I'm not doing very well here.)