Honestly, the most plausible reason I've seen cited is his left-handedness; contemporary accounts of him usually cite him habitually writing and painting with his left hand and non-habitual mirror writing is quite commonly associated with lefthandedness. Leonardo's notebooks in particular were his private notes rather than published and circulated treatises, although they were appreciated and collected even in his time, so it makes sense that when writing them legibility would take a backseat to convenience and facility of writing.