I have wondered this myself. I think it is very very unlikely, but possible. It seems that typically the underlying securities are held by a custodian (in order to mitigate exactly this type of risk). For example, WisdomTree's custodian is BNY Mellon -- or at least was in 2012, see
http://www.sec.gov/Archives/edgar/data/1350487/000119312512255257/d361108d4017f2.htm. So while there isn't much risk in this case of the ETF issuer committing fraud, there is nothing as far as I can tell to keep the custodian from running off with the funds. So I suppose to measure 'Madoff risk' for an ETF is equivalent to what you think counterparty risk of the custodian is.