Hello,
This is not a HikaShop problem, the data in the CSV file is correct. It's Excel that changes it when you open the file. When you double click a CSV, Excel auto-detects each cell and turns anything that looks like a date into a date. In a locale where the point is not the decimal separator, "9.99" is read as month 9 / year 99, so Excel shows "Sep99" (September 1999). That's why only some values are affected: only the ones Excel can read as a date get converted, the others stay as numbers.
You can check it: open the exported file with a plain text editor (Notepad), and you'll see the correct value 9.99. The export is fine, it's only the display in Excel that is wrong.
To keep the prices intact, you have a few options:
1. Export in XLSX instead of CSV. Create a mass action on the products (System > Mass actions) and choose the XLSX export format. XLSX stores real number cells, so Excel never turns them into dates. This is the cleanest solution.
2. Set the "CSV decimal separator" to a comma in the HikaShop configuration (main tab). The prices are then exported as "9,99", which a European Excel reads directly as numbers instead of dates.
3. Or open the CSV without letting Excel convert it: in Excel, go to Data > From Text/CSV, select the file, and set the price column type to "Text" (or the matching locale) before loading. The values then stay exactly as exported.
About your second question, on how to save it: the encoding (CSV UTF-8 vs CSV MS-DOS) only affects accented characters, it doesn't cause the date issue, so keep CSV UTF-8 to preserve special characters. The field separator HikaShop uses is set in that same configuration page ("CSV separator", semicolon by default).