FTR, I am not a fan of general purpose uninstaller programs. I use the application's uninstaller, or Windows own Control Panel applet works just fine for me. If I have a problem uninstalling a particular program, then I might use a special purpose uninstaller, but never a general purpose one. And frankly, I think the cost of that particular uninstaller is outrageous - especially when there are several uninstallers that are free for home, non-commercial use.
Having two drives, one for your OS and one for all your applications offers a bunch of advantages and disadvantages. The biggest advantages are data protection and performance.
If your data is on D drive, and your C drive fails, your data is not lost. You simply restore your C drive, and everything is still intact. If you lose your data drive, you still have your OS (and its all important Registry) and all your drivers on C, then you simply restore the D drive.
With multiple physical drives (not partitions on the same drive), the OS can, and easily does access all the drives simultaneously - for example, to read in a Windows file from C while at the same time, accessing an application file on drive D.
But with a single drive, there is only a single R/W head, single data path and a single drive buffer so OS files and applications files have to be read in sequentially. That takes longer. Now whether you, as the user, "see" that performance difference is another matter - much dependent on how much RAM you have, as well as the horsepower of the rest of the computer. The biggest noticeable difference may just be boot times, and I don't put a lot of emphasis on boot times (unless excessive).
With one drive, you only need to maintain one current image backup. With multiple drives, you will have to maintain multiple image backups.
And of course, multiple drives cost more, use more energy and create more heat.
I guess I should add security as an advantage for multiple drives. If you are the administrator of a computer with multiple users with different levels of access, multiple drives may provide greater security options.
My advice today, with today's monster and fast drives, is the user needs to decide how involved they want to be in deciding how the OS does things. If I want to display my geek flag and be totally hands-on then I will use multiple hard/SSDs and partitions and organize and arrange my OS, applications and data files anyway I want, as if I was filling a room full of empty file cabinets.
If I was looking for total convenience, I would install Windows 7 using all its defaults and leave the single drive in one big partition. Note Windows, and especially Windows 7 is fully capable of managing it that way in excellent fashion! They have had decades to fine tune that OS, and have done that very well.
Bottom line (assuming modern hardware and Windows 7 or Linux),
if you like to fuss with things, use multiple drives. If you don't, don't. But once you choose, that's what you are stuck with.
REGARDLESS how you configure your computer and drives, you still need a reliable backup program. So all concerns about imaging this or that with this drive configuration or that drive configuration seems moot to me. You still need a reliable backup program, whether you backup/image one drive or two.
Where you might run into problems is if you install to D: and later decide to change the whole drive to drive X:, then the logs say it's on D: but now you have no D:, you have an X:
Very true. But to clarify, that has nothing to do with multiple drives or partitions. If you install on C: and later decide to change the whole drive to X, you will have the same issues.
But note that is only for applications or programs - software that loads bunches of individual files. The Registry on the boot drive (most likely C drive) must still show the correct locations. The actual data files (Word docs, mp3 files, jpg image files etc.) are still accessible via Windows Explorer or the main apps Open/browse menu if not in the application's default file location. They will not however, be found under My Documents or Libraries - at least not until that is manually updated and the defaults changed.