You've asked three different questions about three apparently different kinds of items: emotions, concepts, and physical things. So there may be as many as nine different answers, depending on which question is being asked about which kind of item (and some of those nine answers may be of the form "It depends"). I'll choose just one of those kinds -- concepts -- and try to answer your three questions about it.
1. It's controversial just how concepts themselves exist, but it's clear that a concept can be instantiated -- there can be instances of the concept -- even if the opposite concept isn't instantiated. Take the concept self-identical. Everything instantiates that concept, because necessarily everything is identical to itself. But nothing instantiates the opposite concept, self-distinct, because nothing could be distinct from itself. Or consider two more controversial examples, the concepts physical and nonphysical. Some philosophers say that everything is physical, so clearly they think that the concept physical is instantiated while its opposite, nonphysical, isn't (and maybe couldn't be) instantiated. Other philosophers have said that everything is nonphysical, so they hold exactly the reverse view about instantiation.
2. We can recognize self-identical things -- it's easy! -- even though we can't possibly recognize self-distinct things (there being none). Ditto for physical things, according to some philosophers, and nonphysical things, according to other philosophers.
3. I'd also say that self-identical things existed (such as meteors and dinosaurs) long before we arrived on the scene, and plenty of self-identical things exist of which we will never become aware. It's a big universe, and it will outlast us.