For a brief time they had restrictions on the languages you could use. That was a reaction to Adobe shipping a tool to compile your Flash source into an iOS app. But that didn't last very long.

That said, if you're dynamically interpreting code at runtime that was downloaded from the internet, you're only allowed to do that using JavaScriptKit. You cannot, for example, embed the Lua interpreter and then interpret code downloaded (but code in your app bundle is fine).