Actually i have done this since the first day i started to use Adobe Photoshop started with 6, 7, CS, CS2, CS3 & now CS4 with no issues.
As i said. I have done this all the way trough all suites and never had a single issue with plugins, filters, actions, scripts, updates, uninstaller etc. etc.
Infact all photo related applications i use i place in the Photo application folder i made my self. Adobe Suite CS3, CS4, other Adobe apps, QuarkXpress 8, Aperture, Adobe Lightroom 2, Capture One PRO, LightZone, Photo Mechanic, Noise Ninja 2.x and more and i dont have any problems what so ever !
BUT, i use the installer to place the apps ofcause. I dont move them after, that would be crazy sure enough.
I also do this with all maintenance applications i use. I have a folder called maintenance.
Cocktail, Leopard Cache Cleaner, SuperDuper!, File Buddy 9, DiskWarrior, TechTool Pro 5, Data Rescue II, Hardware Monitor, more, more, more also without problems.
So i dont really know why i should stop doing this now since i have done it from first OS 10.x
I am sure if people move folders around after it is installed, it will be a big mess. But i always install the apps with the installer to the right locations i want.. No problem.
Its not because i dont trust what your saying, and it would maybe run better on your system that way. But i have never had a single problem with the way i do it.
Just for information :-)