As an example, this NUC D54250WYKH has a Mini DisplayPort 1.2 and a Mini HDMI 1.4 port. The specifications of those interfaces would allow to drive 2560x1600 each. The built in intel cpu has a HD Graphics 5000, the Display port is guaranteed to drive 4K displays and multi monitor solutions, but there's no testament to the capabilities of the HDMI output.
Most of the 2560x1600 (or 2560x1440) monitors do not accept their native resolution on HDMI inputs. For example the Dell U2711 accepts its native resolution on DVI and DisplayPort only, not on its HDMI input, as described on page 33 of the manual "Set the screen resolution to 2560 x 1440 (DVI and DisplayPort) or 2048 x 1152 (VGA) or 1080p (HDMI, Component).". The Samsung SyncMaster 27A850DS does not even have HDMI inputs and accepts its native 2560x1440 on either of 2 Dual Link DVI or the Display Port.
On a side note: This older 3rd generation NUC DC53427 has two Mini Displayports and one mini HDMI ports. While its manual does not explicitly list support for the dual WQHD resolution on the two Display Ports it does not restrict them either. If all three ports are in use, the three monitors can be driven to 3 times Full HD (1920x1080). This implies that there might be a restriction on driving two WQHD displays at the same time on the two Display Ports.
intel FAQs related to this topic are the Standard Graphics FAQ and the 3 Monitor setup FAQ. The 3 Monitor FAQ is very specific on combinations of resolution, but the 2 monitor/extended display FAQ is not.
I would need to run the system with both Windows 8 and Linux, but if any one of these would drive the dual WQHD resolution on the NUC hardware, that would be valuable information.