It's fine to use new as long as you're immediately sticking the result in a smart pointer. But yes, delete should be very very rare in modern C++ code.
It depends. The trick to using new correctly is to put it in a function whose sole purpose is to immediately store new's result in the smart handle. I.E. You're writing a function that's analogous to the make_unique function.
You might need to do this if you're implementing your own smart handle or writing a factory function for a class with a private constructor (make_unique will not work).
Off the top of my head, I can't think of any good reasons to use delete.
If your handles are pointer types, you should still use unique_ptr, you just need to give it a custom "deleter". (Of course you should probably still encapsulate this in a function like make_xxx() just to avoid the potential mistake of not supplying the correct deleter everywhere.)
