Yeah, I was really surprised when I rolled that 19. But, I realized in the prior encounters the two skill Vecna would most benefit from would be Athletics and Stealth.
He is too easily grappled. Inside that Anitmagic Field he can't escape it either. That led to his first loss IMO. If he had Athletics, he would have been +10 and could likely escape even two grapplers eventually.
And stealth is very valuable when you can teleport away, out of line of sight, and then hide. But at this level without proficiency the PCs would too easily spot him.
Honestly, for a creature 1000's of years old, I would expect Vecna to have as many skills as he wants.