According to the polkit documentation, numeric prefixes determine the order in which rules are processed.
Although it is recommended to use numeric prefixes, most of the preinstalled rules in /usr/share/polkit-1/rules.d have none, so using any numeric prefix for custom rules elevates their priority above the others.
This indicates that the rule priority is irrelevant unless you want to override the defaults.
As far as I understand, there shouldn’t be any performance drawback as long as you don’t create huge rules sizable in megabytes of text.