Yes, it is is common, but I don't think it can really be a cliche. However it there are cliches associated with it. One that I commonly see is an orphan being "special" or being sent to live with an unusually distant relative.
I've always figured that the parents are usually killed off so the author doesn't have to deal with them. Especially if the protagonist is young, in many scenarios, the first question would be "where are the parents with all of this going on?" It enables the focus to remain on the child/teen, and especially in books that are written for children and teens, part of the fantasy is not being constrained by parents. So, I don't see it so much as a cliche or stereotype, necessarily, as much as I see it as a writing device/mechanism.
A stereotype often has a base in character design. Take that and branch off from there into the Why's Why does he feel this? Why does he do this? Even if the answer is simple or complex, a character comes into shape when their traits are given context that can be explored
Even when writing a stereotype, like a high school asshole with rich parents (which I’ve done, except he was in college), when you approach the character as a real person, I’ve noticed that the stereotypical, cardboard-y traits kind of melt off. If you are writing a character realistically, dictate his actions by his wants and needs instead of the plot’s or the two-word trope-definition you can find on tvtropes.org, it might not turn out all that stereotypical after all. I’ve also noticed that some people become self-fulfilling stereotypes, especially in high school. They want to be identified as the mysterious, pale loner poet (even though they’d like to go to the beach and surf), or the asshole quarterback who gets all the girls (even though he also loves cooking shows), or the fragile push-over geek (who’s actually into medieval combat), so despite trying to fit into some mold for identity reasons, they are still bound to have traits and interests that clash with the stereotype they wish to portray. As for the orphan thing. Dave Egger’s Staggering Genius gave me some new perspective to the “trope.” People get orphaned, it happens, and if a writer puts enough effort in it, they can find an angle that makes the character come alive, makes it multidimensional.
