No, it won't affect anything like that. If your system databases data files are on your system drive (for example in C:\Program Files\Microsoft SQL Server\....) then I would recommend moving them to a drive dedicated to database files. This ensures that SQL Server doesn't get choked by growth of things like application logs, and conversely that any growth of your system databases won't eat up all the disk space that the operating system should be using. You may find that your msdb database grows quite large, especially if you don't control your job, backup and maintenance plan histories.

John