Normally, frapper de is employed mostly in figurative senses, e.g. for juridical rulings, but also to mean "inflict" (frapper de stupeur "stupefy", frappé de folie "rendered mad") etc.
When the verb is used in its physical sense ("hit"), the default preposition is indeed par, unless the instrument is a body part, in which case, indeed, de is the regular construction. Other construction in French are specific to body parts, but not many involve alternate perpositions.
It is common cross-linguistically for constructions that involve body parts (usually because they involve grammaticalized inalienable possession) to have peculiar constructions applying to them.