As stated above read whats happening in the fragrant harbour forum and you will see that there are problems with both options.
CX does have a union of sorts, which EK does not. CX does not have fleet pay or rotating seniority etc They are different in many ways, lifestyle included.
CX does now employ rapid command pilots onto their freighter fleet and they have plenty of disgruntled F/O s just like EK as well.
EK does/did? have ex cx pilots working for them and now a few retired cx DECs as well.
I can't imagine that there are too many other EK pilots heading off to join cx as a S/O, so don't think that is a sign of anything definnitive.
Cx to their credit do offer their employees overseas bases which EK don't and we all wish they did.
There can be problems for many people after a time out living the expat life and cathay have found ways to keep senior employees working for them in a cost effective manner from their home countries.
Go to the interviews and decide on what is important to you not what other people might think.
There are many happy, contented pilots working for both airlines, but you will not find that many on pprune because they are probably off enjoying themselves, that leaves the rest of us who have issues to work out and pprune can be an outlet for many peoples frustrations.