I own reference and aftermarket 290s.
In a decently cooled case, at stock speeds, under normal loads (not mining or Furmark), the difference is undetectable (zero to minimal throttling) and it's not much noisier than a stock 7970.
The difference is if you want to overvolt/overclock heavily, then you should either be okay with cranking up fan speed an noise, or go with an aftermarket design. But I would not pay a huge price premium. Keep in mind that a 290 is still one of the fastest GPUs on the planet even at stock.
Also, keep in mind that aftermarket parts need to breathe and suffocate in crossfire. Well, one of the cards gets flowing air but the other probably has less than an inch gap between it and the hot backplate of the 290 beneath it. That suffocating card will suffer reference or non-reference. In fact the reference card might actually be better since it's a powerful blower design so it WILL get its air, even if it has to generate more noise to do it. Whereas an axial (non blower) fan will struggle.