It's not just commands that are actual for the current session (like ls/cd/cat), it's also incorrect commands or just commands not worth retaining still being saved among with the useful commands.
The most precious is user's time. And when you fzf part of the command with the regularly saved history and would like to re-execute something important - you'll first get a long list that you'll first have to filter to find the command you were seeking.
So to counter your question with another: why store garbage?