Is it still an "ice cream cone" if it doesn't have ice cream?

yes, the cone is an ice cream cone because it is a cone that can hold ice cream.

And it is a Soup Bowl with candy in it. You are describing the bowl to differentiate it from other bowls.

It is common to use nouns as modifiers of other nouns. The term ice cream serves that adjectival purpose, modifying cone.

The waffle cones and sugar cones that are traditionally used (at least in the US) to hold ice cream were designed for that purpose. While the cones could be, and are, used to hold other things (and may even be eaten plain, if one is so inclined), their most common usage serves to define them, regardless of how they are otherwise used.

When they hold frozen yogurt, they still are ice cream cones. Filled with jelly beans, likewise. But note that the cones are often referred to without the ice cream qualifier. They may be called sugar cones, waffle cones, cake cones or simply cones, as in the ice cream vendor's query, Cup or cone?

Many other noun/noun terms keep their primary designation even when the item is put to purposes other than those described in the modifier. A car park is still a car park even when there are no cars on it and it is being used to host a fair.

The dividing line is between a noun being used as a casual modifier and a noun/noun phrase becoming an established term is not bright. By definition, the primary noun has other uses or no noun modifier would be needed. But when a relatively fixed relationship has been established such that the modified noun now has a distinct and relatively stable meaning, the modified name sticks, even if the item is put to another purpose. A tea bag applied as a poultice is still a tea bag.

There's no hard and fast rule, it is a matter of utility. You want to refer to the object in the way that will best help the listener identify it. The other day I saw a stand at a festival selling an "ice cream cone full of fruit." In this case we have a well-known object with a new use. It would be harder to understand the reference if I called it a "fruit cone." On the other hand, you wouldn't refer to it as "the soup bowl full of candy," because it's easier in this case to identify the bowl by its function.

A glovebox is still a glovebox when it doesn't have gloves in.

A rubbish bin doesn't change name when you empty it.

A handbag isn't called a bag when you put it down.

Objects are named according to their general usage, not the exact usage at the specific time you refer to them.

It is still an ice cream cone.