Sure, though in the grand scheme of things that penalty is pretty small when compared to the DOM operation itself. Eg. doing an appendChild() on an attached element and causing a reflow.
It depends a lot on what you're doing — if you're hitting fast-paths (esp. if you're dealing with out-of-tree nodes) it's entirely possible to end up with the JS/C++ trampoline being a significant part of the bottleneck, for much the same reasons as why Array.prototype.reduce can in several implementations.