There just aren't that many widely used applications that deal with things like this, but Google sheets seems to be the obvious one.
For me personally, I usually view things in Excel/LO but don't save, and if I need to modify anything I'll use a text editor for one-off changes, or I'll use something like Python with the pandas library for more programmatic changes. Pandas does have issues forcing timestamps to convert sometimes, but that can be easily configured. Otherwise, no problems with this method.
There's definitely a lot of friction if you want to edit .CSV's without your formatting/encoding being altered, unfortunately.
LibreOffice does a similar amount of clobbering, but in general it notifies you of any would-be clobbering and allows you to abort beforehand, which is really nice. I still avoid exporting via LibreOffice though for very sensitive situations, but it is noticeably better still.
I always view CSV as a lowest common denominator, of course more precise formats exist, but not everyone can use those. Csvs normally get the job done, but like anything else you need to know it's limitations. Something like a basic phone book should work, your scientific data, with dozens upon dozens of floating point numbers may not work.