"Do I have to write wrapper functions for all built in functions I want to call by reference or do they want me to entirely stop calling by reference?"
No wrapper functions, you should never have called those functions by reference in the first place really.
You will have to start using the functions 'properly'.
Depricated means that they plan to abolish it in some future release (and quite rightly so I might add, especially with octdec it makes NO sense at all to allow passing by reference)