I would never recommend that anyone do any sort of "cleaning" of the registry outside of the very targeted and specific removal of malware related entries that are removed by programs like Malwarebytes. There may be other, isolated, and equally targeted examples such as the upper and lower filters issue that prevents ODDs from working, but beyond that I do not see any particular need for these programs.
If a program leaves little bits of itself behind when you uninstall it, at most we are talking about a loss of space measured in bytes, and the performance hit you might suffer would be probably a fraction of a nanosecond. Compare that to the issues that can be created by an overly aggressive registry cleaning program.
I also find it rather suspect that, to the best of my knowledge, there are no open source registry cleaners, and the registry cleaners out there will not offer up any details on the criteria the program uses to determine if some entry should be deleted or left. There are also plenty of registry cleaners which will claim there are hundreds of errors on a virgin Windows install. The final nail in the coffin as far as I am concerned, is that Microsoft created the first registry cleaner. When it became clear that the program created problems with MS Office, it was pulled from their website, and in the many years since then, it has never been reworked and offered up for download again.