I came across
０９年度, and while the meaning is clear I didn't know the actual way of reading it. My first reaction was
ゼロさんねんど, but I have no way of checking if that's right. I thought it might also be simply,
さんねんど, but again I can't tell.
I think we usually read them as さんねんど, きゅうねんど etc. I've never heard anyone say ゼロさんねんど or ゼロきゅうねんど. I think we write that way to differentiate （西暦/A.D.）０３年度 from （平成）３年度.