Also I don't think he'd have "rouge" applications there Seth, ol pal. Unless he likes his cheeks all rosy.

Plus one for CCleaner.

The time it takes to find a registry value does indeed increase as the hive grows, a basic characteristic of hierarchical databases. When SONAR requests a registry value, specifying the path does not mean Windows can instantly zero in on the key's physical location in the file. Every search involves scanning, entry by entry, until a match is found. I do a lot of benchmarking of this kind of thing, part of the process of optimizing my own code.
 
The scan, however, is pretty durn fast because the registry is cached. But it can still sometimes be a bottleneck. Remember, a program such as SONAR (and its hosted plugins and the Windows functions they call) will typically make dozens or even hundreds of registry queries in response to you just clicking one button. More involved processes such as program initialization or a plugin scan will require literally thousands of registry queries. Even if each one takes 1 microsecond, they can cumulatively account for several seconds' execution time. 
 
So registry reads and writes are relatively expensive, and get more expensive as the registry grows in size. Sounds like a good argument for a registry cleaner, right? But no. Registry cleaners remove such a small percentage of the total data in the registry that any minuscule speedup they might achieve would be irrelevant. Given that they're so prone to breaking something, the risk:benefit ratio just doesn't pencil out.
 
So the bottom line is: skip the registry cleaner.

Well, if you've worked in support for a billion years, chuck the advice of likewise experienced folk and are aggro about it the simple answer is that you sound stubborn and incorrect. But hey, evidence can be wrong too I suppose.
 
Personally I'd dump the scattered VSTs. I doubt you're getting a major speed increase from them and obviously having them scattered across partitions is screwing yourself. Make a clean install and start from scratch. Besides, you can always install the VSTs themselves on your C drive and sample libraries on another drive, that's what most of us do. (and where the more taxing loading comes in anyway).
 
That said, here'st he utilities I use after using just about everything out there under the sun:

• MSSE (yah, Windows own virus protection...after using about 20 other products over the years it's the one that gives me the least headache)
• MalwareBytes (just as a backup in case MSSE misses something...I haven't had to run it in a LONG time)
• Auslogics Disk Defrag - I used to use Windows own, then the one that came with System Mechanic before it got bloated. This one is fast and does the job, and can run on several disks simultaneiously. I run this once a month or so
• CCLeaner - I use it for trash but also for it's registry cleaner. I used to use several other ones, but this one is fast and clean and I've never had a problem with it screwing with VSTs. It lets you back it up in case there are mistakes but I've never had a problem. 

Now you can curse and spit and tell us we're wrong, but we're also not having the problems you're having, so I hope you'll consider that data as you evaluate your solution. Oh, I suppose there's one other huge difference in my rig over the last decade: I don't use warez anymore. I used to, admittedly, back in the day but once you're on your feet and making money with a DAW they just hold you back with all sortsa problems. Since "going legit" I've been blessed with relatively rock solid builds. Take from that what you will.
 
 

There are numerous things that can compound together to reduce system performance (one big contributor is people tweaking things without realizing the system impact). A utility you may want to run is Iobit's Advanced System Care (free version). I have the paid version, but the free version is rather capable for top-level tasks. I would recommend running the whole gambit on the "Scan" page, but don't defrag an SSD if you have one.
 
I had a work computer a few years back that was older anyway, but ran like a lame dog. So I took ASC to work on a thumb drive one day and the free version found 10,000+ issues on that machine (in an "IT Security" company no less... what irony!)

To the OP,
 
It's possible you are just using a poor registry cleaner.
 
I've used the registry cleaner in JV PowerTools for years, and it's never harmed any of my systems, much less any component of Sonar.