Hmm, weird. It definitely isn't deprecated now, according to the docs[1] and I haven't seen anyone complain about ipairs recently ever since I learned the language ^^. But anyway, the only real downside about ipairs is efficiency so even if they removed it I would probably just add it back myself as a regular function.
http://lua.2524044.n2.nabble.com/petition-to-keep-ipairs-ali...
Edit: both are from 2010. This never became final perhaps?