A while back I relocated all of my music related software and linked everything through directory junctions (Windows 7).
 
I thought this would be transparent/invisible to all installers, but it's happened on many occasions that after updating a program, the directory junction is gone and the folder itself is in C:\Program files, etc.  The other programs from the same company are still where I put them, but the new one or update is on C: and the others can then no longer be found by that company's software manager.
 
This just happened to me again installing Kontakt 5.  My directory junction in C:Program Files is gone, replaced by a real folder "Native Instruments" with only K5 in it.  My other NI stuff is still elsewhere where I put them,  but can no longer be found.  I had to (as on other occasions) move the new files (K5), delete the NI folder in Program Files and recreate the directory junction to point to my location.
 
This has also happened at least with Waves.
 
Is this because the software manager completely deletes the existing folder (which is in fact a directory junction) and recreates for the update ?  This doesn't make sense because the other items from the same company have no reason to be deleted/touched.
 
Or perhaps this is a problem with my french version of Windows in which the "Program Files" folder (for example) is itself accessed through a hidden directory junction to rename it to "Programmes".
 

This isn't much help but I've not had a problem with my Junctions.
mklink /j "C:\WhereIWantItToAppear" "D:\WhereDirectoryActuallyIs"

I had the exact same problem just a few weeks ago. I have moved all my VST2 plug-ins from C:\Program Files\Cakewalk\Vstplugins to C:\Vstplugins, as I now use multiple DAWs. To make a smooth transition I also made a directory junction pointing to the new location.

Everything worked well for months until one day I noticed that almost all my plugins had been disabled in my Plug-in Menu Layout. The only ones enabled were those from Applied Acoustics, which made me believe that it was the recent update of my AAS Modeling Collection which most likely replaced the symbolic link with a totally new and very actual folder. The only files found in C:\Program Files\Cakewalk\Vstplugins were those plug-ins from AAS.

Once I realized that all my other plug-ins were still available in C:\Vstplugins it was no big deal fixing the problem. But it made me quite uneasy as I didn’t know this could ever happen.

You can't predict what installers are going to do, including such unexpected actions as deleting an existing folder (and its associated junctions) and creating a new one. I've had battles with NI (and others) in the past, and years ago just surrendered, allowing products to install wherever they like. It avoids a lot of headaches.
 
But, you say, I don't have room on my C: drive for everything! Well, maybe, maybe not. All my music software - multiple DAWs, Spectrasonics, Superior Drummer 2 and 3, Native Instruments, plugins and virtual instruments - take up only ~6 GB. Not a significant percentage of my 500 GB SSD. Why so little? EXEs and DLLs don't take up much space, so they get to stay.
 
The way I got the C: footprint relatively small was to move only the largest files (meaning samples) elsewhere, leaving the main installation alone. Kontakt, for example, can live anywhere it likes but because it always respects the location of my Kontakt libraries, I can keep all of them on a 1 TB (and nearly full!) dedicated sample drive. Whenever I run an installer other than Kontakt instruments I just accept the default paths and click OK.
 
Junctions are only needed for a few instruments' libraries (e.g. the Cakewalk instruments and Omnisphere), but not for two of the biggest ones (Superior Drummer and Kontakt). 
 
I'd recommend getting the free utility WinDirStat, which clearly displays which files and folders are eating up the most space. That'll help you decide where the best bang for the buck will be when deciding what to relocate.

bitflipper
 
I'd recommend getting the free utility WinDirStat, which clearly displays which files and folders are eating up the most space. 

Great program. I have been using it for years. Recommend it highly. Does it's job well. No nag screen. And free. I have it open right now getting some things straight on my external drive.