Usually, the "X" is pronounced as a "Z" sound (like in xylophone or xenophobia), but in this case only time will tell.
It depends on if they want the letters they are using for the version to be attached to the sound of the Pokemon themselves. If so, then you'd have "EX-erneas" and "WHY-veltal". Otherwise you'll likely have "Z-erneas" and "E-veltal".
I can see either being possible really. Be interesting to know the name etymology. I always enjoy reading those.