So generally words with a yist sound at the end are represented with an iest suffix, for example scariest or crappiest.
However the word hobbyist is not.
Is there a defined reason for this? I can't find another example like it.
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As others have said in the comments, your problem arises from the suffix used.
Hobby, lobby + -ist -> Hobbyist, lobbyist
Crappy, scary + -est -> Crappiest, scariest
If you tried to remove the 'y' from hobby you would end up losing the sound, clearly hobbist doesn't work.
Your other alternative is to change the 'y' go and 'i'; hobbiist is definitely not nice.
All this leaves you with a much nicer alternative of hobbyist
The difference between words ending in -ist and -est is one of the meaning of the suffix.
Which suffix is used has nothing to do with the sound at all.
Whether -y becomes -i- when a suffix is used depends on the suffix: it does happen with the comparatives -er, -est or with certain agent nouns like multiplier; but English will never change -y to -i- when what is added starts with an i. Hobbyist is not spelled hobbiist.