Copies of spells are spells, yes. There are no instances where copies of spells do not count as spells (because they are spells, in every way). What you're probably thinking of as not interacting is what will also apply to your specific question. The copy of the spell may be a spell, sure, but that doesn't mean it was cast. Mindbreak trap cares about number of spells an opponent cast this turn. Replicate, Storm, and Mirari all copy spells and put those copies directly on the stack, the copy is never cast, so won't count as a spell cast for anything that looks at that (including Mindbreak Trap's alternate cost requirement)
Any time a spell is copied, the copy is put directly on the stack and not played. When a copy is cast, the effect will tell you to copy the card then cast the copy. Compare the wordings on Isochron Scepter and Mirari to see the difference.
Isochron Scepter

|Artifact| Imprint -- When Isochron Scepter enters the battlefield, you may exile an instant card with converted mana cost 2 or less from your hand. / 2, T: You may copy the exiled card. If you do, you may cast the copy without paying its mana cost.
Mirari

|Legendary Artifact| Whenever you cast an instant or sorcery spell, you may pay 3. If you do, copy that spell. You may choose new targets for the copy.