The giant head-bump thing is common in other anime (and media, at least in East Asia), and is used to indicate an injury to the head, as you've stated. For instance, a Chinese search for "撞头" on Google Image (literally "hitting head [on something]") gives images such as this one, which don't seem to be connected to any anime:
I am pretty sure I have seen this in other anime before (e.g. Keroro), but I'm having trouble locating similar screen-caps. In a sense, it has become something of a "convention", the same way sweat-drops are kind of a "convention", which explains the usage here.
Thus, the Naruto extension of this to inanimate objects appears to simply be an extension of this trope -- the objects have been "injured", and so like the heads of these individuals, swollen, overly stylized bumps form on them.
TV Tropes calls the head case a "cranial eruption". However, any searches for the term don't produce many results beyond sites like TV Tropes (and some similar site), and this small anime wikia doesn't seem to have a listing for the trope, despite it being a fairly prevalent thing. (Conversely, it doesn't have "ahoge".) So it seems that there's no real, generally accepted English term for this trope.