He never goes into how he uses Lua, but if he's still targeting Apple's libraries (rather than some cross-platform transition layer), they might not even be able to tell he is using Lua in the first place.
It may also be worth nothing that the particular case of Lua was already prohibited under the iPhone DPLA section 3.3.2 which states that no interpreted code may be included unless it's run by Apple's interpreter(s). Wax embeds a third-party Lua runtime that does just that.
That said, there was talk about moving Wax to llvm-lua such that the resulting application would be compiled machine code. The new clause precludes this option entirely.
The only uncertainty left, now, centers around enforcement. There are a number of PhoneGap and Wax powered apps already in the store, and PhoneGap was even blessed as an approved framework. Only time will tell if that blessing stands.