Since r12486, templates within user signature are always substed (by automatic modification (see Parser::cleanSig) upon saving of user preferences), which is probably meant to decrease the server load.

However, since {{subst:X}} substitutes only the first level of template transclusion, this feature is very easily circumvented: you only need to create a page containing the desired template call and use this page as your signature.

The most straightforward idea how to solve this could be to introduce the desired {{substall:X}} functionality (see T4777: Provide a recursive subst: function in the PST – {{substall:foo}}) and use that instead of plain subst. Or, you could maybe ensure the full recursive substing during parsing of ~~~[~] (somewhere around Parser::getUserSig), but I guess it would be not much compatible with the current parser design.