Hello and welcome to the AmiKit Support Forum.
Short answer: NO.
I use Windows folder system from the very beginning and I have never experienced any problem with Windows files, partitions or whatever.
No matter whether you use hardfile or folders, the path to AmiKit system partition is strictly set to the folder where you installed the AmiKit itself. And, if not set otherwise, you cannot access any other paths or partitions from the AmiKit enviroment.
However there is "Add PC drives at startup" option enabled by default in AmiKit/WinUAE settings (regardless whether the hardfile or folders are used) which makes the Windows partitions visible in AmiKit desktop. If you want to make sure your Windows files keep intact, disable this feature.
What about viruses? I would be relaxed. If you browse internet or manipulate files in AmiKit environment, you cannot be infected by any known or unknown Windows virus. Simply the Windows virus cannot get activated in Amiga environment.
Fragmentation? Yes, that might be the drawback compared to hardfile alternative. Maybe you can install the AmiKit on a separate partition to avoid the fragmentation?
Anyway, storing the AmiKit files in Windows folders has some advantages compared to hardfile IMHO, eg. you can always access the AmiKit files without the need to start the emulation itself (this is something what manual AmiKit updates do if necessary).
If you prefer the hardfile anyway, here's a guide how to convert AmiKit to hardfile