It hasn't been explicitly mentioned, maybe it's obvious among professional DR technicians, but it might not be for anyone reading this : if it's a SSD, the "Trim" feature is probably the reason why most of the deleted data has been effectively wiped clean.
Have you tried opening the volume with an hexadecimal editor, to see roughly how much of it is just zero-filled ? What did you observe in R-Studio, is the file tree complete, including the missing files, although most of them are actually empty, or are those files missing in the file tree as well, meaning their MFT records are gone too ? The second hypothesis would be more surprising.
Are the lost files of a common type (JPG, DOC...), or a very specific type ? Either way you could attempt a raw file recovery, but R-Studio does that by default so most likely you already had everything it could find (be sure to select the right file types in the options though, according to what should be expected / what there used to be ; you can also define specific header recognition patterns if some files are of a rare type unknown to R-Studio). You imaged the drive before running R-Studio on the image, right ? Otherwise, the time it took to scan the drive must be added to the power-on times you mentioned (unless there is some trick to disable Trim ?).
Is there some kind of a tool, where I can find files in the System (Windows 10) that doesn't belong to the system? I'm sure there is some kind of a database of knows System and Programm files. But do you know how I can get it?
I'm not sure of what you mean exactly here. Are the missing files .exe or .dll or .sys ? Probably not. On my Windows 7 install, these three files types amount for 64% of the total size of the allocated files, according to WinDirStat a simple and free but efficient space visualizer. Then, by decreasing order : .dir, .db, .msi, .tmp, .mv_, .edb, .cab, .dat, then it gets below 1GB / 1%. More common user-generated file types are much more rare within system and softwares files : .jpg and .pdf amount for about 500Mo of each ; .xls, .ods, .cls : ~2MB each ; .doc, .xlsx, .pptx : only 100-200KB each (not a single .docx).