If I have an Alolan Raichu with Speed Energy attached or a Starmie with Wash Energy attached, if I use their "Electro Rain" or "Multishot Star" attacks and discard those Special Energy cards would it get through Duraludon VMAX's "Skyscraper" Ability or not?

Because you don't know how many targets to select until you discard all the Energy, the process is to discard the Energy first, then choose which Pokemon take damage, and then apply damage. Since for those particular attacks the discard happens first and THEN damage is applied, as long as there are no other Special Energy cards attached to Alolan Raichu or Starmie the damage would not be blocked by Skyscraper.

Relevant cards

SWSH7_123

SM11_57

SWSH8_53

SWSH2_173

SWSH4_165