It's not true that everything is a list in most languages. Typically an AST is built with both lists and structs. Special forms are always going to exist and the code needs to deal with them, so this isn't a loss; it's being more explicit. Well-named fields are better documentation and faster than accessing the nth item than a linked list. (You can emulate named fields using just lists, but it's just a convention.)

Also, in most languages, the lists aren't linked lists. They're typically array-backed.

JSON has both lists and objects (which serve as structs) and it's quite popular and usable for representing AST's.