Crota does have a mom. It says so in XXXVI. If oryx was a girl at some point, it was before Crota was born.
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The only way for this to make sense is if hive aren't born through normal means. (Normal meaning like mammals.) If they DO come about like mammals, then Oryx gave birth to Crota -> worms turned hive into what they are now -> Oryx is turned into a male in the process.