The stock database has relied to a considerable extent on the values found in Harpoon paper rules.
Where they didn't exist, my best estimate was made after comparing to similar weapons, warhead type, warhead size, etc.
Variation between facilities with the same runway size is typically attributed to whether the facility is civilian or military, in which case the latter would typically have hardening measures implemented to its infrastructure, including hardened aircraft shelters, bunkers, etc.