No - the text variable in a running header is one single code, and InDesign cannot change the formatting of individual words anymore.
But in your case the solution is real simple: capitalize the text as you need in the title. Then, only for the title itself, set its Capitalization to All Caps.
Set your heading in upper and lower case
Podenebne znacilnosti obcin Postojna in Pivka
In that paragraph style - set it to all caps
Insert your Running Head Variable
Set that to a paragraph style - and don't set the Case in the style.
@premio_oscar thank you for tricks