I tested a piece of Afrikaans text I wrote in Scrivener 1 in the beta to see how the spellcheckers compared. The spellchecker flagged some common words with diacritics that aren’t flagged in the old Aspell version.
I also tested the same words in LibreOffice - which should have the same dictionary files - and the words were fine. Some of the words were present in the dictionary without the diacritics and they aren’t Afrikaans words like that.
One of the problems is that the dictionaries in LibreOffice and Scrivener may be of different versions (Scrivener’s aren’t necessarily the latest). However, you can use the one to replace the other. I haven’t mucked with Afrikaans, but I have replaced my English dictionary. I think the old thread is https://forum.literatureandlatte.com/t/some-issues/42968/7. Note that thread does not reference Afrikaans, so you’ll have to do some translation. To use LibreOffice’s dictionary files, you’ll have to find them first (or download from the Internet; there’s a site where they can be found), and then use the zip tool to unzip them. this should give you two files: one a .dic file, and the other a .aff file, with a possible third file (a README file that must be present to fulfill the terms of the hunspell license). Those two files you may copy verbatim into your Scrivener/hunspell/dict/Afrikaans-af-za/ directory. For Scrivener to use them, the files must be named EXACTLY (including caps and all punctuation) the same way as the original files are named. I usually rename the originals as (for US English) en-US-OLD.aff and en-US-OLD.dic (so I have the original spellings handy), then rename the new files, and then delete the old ones. Scrivener should be off during this replacement, although it may not matter.
I hope that helps. I do this fairly regularly (every new version). I really wish there was a utility to make it simpler, but there isn’t.