Whether those edges are noticeable when they account for less than 1% of your execution time ... ?
keep in mind that there is a higher property-name resolution cost on prototypes than there is on own properties. If a prototype get chained 2 or 3 (or 20) levels deeps, there's a lot of potentials to strike off the list before the correct prototype appears.
Could you show us what inheritance pattern(s) lead to this sort of prototype chaining? I'd be interested to benchmark it.