Thanks for posting your file. It's not exactly what I was aiming for though. These radially placed cubes were just made to cut the the square holes in the big crescent shaped part and not to become pipes themselves. But I guess your approach might help me to achieve what I need. I admit I'm still a noob who's limited to few known functions of FreeCAD. I'll take some time exploring functions you've used in your approach. Thanks a bunch.
BTW: I might have overcomplicated the design but it does not explain the failing boolean operations. In your approach one of pipes seems broken as well.
[EDIT] Nah... Boolean's Cut with an array make the whole crescent shaped body disappear completely.