Pywikipedia is not the only software that bots use, no. MerlIwBot has its own Java framework and does not use pywikipedia whatsoever. On most projects though, pywikipedia is used by 80-99% of the bots.
Bináris and Andre Engels have volunteered to make pywikipedia compatible with wikidata. Bináris said on the 24th of July that he is busy, in a response from Lydia to translate the Wikibase extensions into Hungarian. Since no progress has been made on that on translatewiki, I am going to assume that he still is busy.
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