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.