The "recombination" frequency of two independent linkage groups (chromosomes) is defined as 0.5 because of Mendel's Second Law of Independent Assortment.
From wikipedia: "any alleles that are completely unlinked (e.g. alleles on separate chromosomes) have a 50% chance of recombination, due to independent assortment."
A recombination frequency of 0.5 implies two genes are "unlinked," regardless of whether they are on the same or different chromosomes.
You calculate it in the same way as you do for genes on the same chromosome. If two genes are in linkage disequilibrium even in this condition, it may mean that they are involved in the same function. Note that you don't need to know whether two genes are on the same chromosome to calculate their genetic distance; in fact, Morgan's student Sturtevant did not even know the concept of chromosome when he coined the definition.
aside from the Chromosomal abnormalities there is no recombination/crossing over between two non-homologous chromosomes, so the genetic distance has no meaning here.