Ok, by using only BOM table it works. So my guess is that using BOM > BOMVersion instead of BOMVersion > BOM relationship will work :) Will check it now.
UPDATE: The problem (if I can call it so) was in the query that is being used by the view that is used in cube's perspective. The very same view returns data that is being expected in AOT and Enterprise Portal, for example, but it doesn't work correctly when used in the cube.
So problem was in using BOMVersion> BOM datasource hierarchy in the query, when it should have been used other way around - BOM> BOMVersion. As I have said, both ways works when testing the view in AOT at least. Don't know if that's an easy mistake to make or not, but hopefully this will help someone.