You ever be dating a girl with hair extensions and try to run your fingers through her hair? And that's how you found out she had extensions? Surprise! Hair extensions are bullshit.
It would depend on how long the joke goes on and to what extreme.
"5 minutes super confused, until I look at my phone" = okay
"An elaborate prank where she changed all the dates that lasts 20 minutes = okay
"A day of being told my family died, world ended, etc" = not okay.
As someone who doesn't like April Fools', I see your point. This plays with the trust of their relationship. However, if the trust is solid and there is a mutual understanding of how they can play with that trust, it's probably fine.
I guess it depends on the couple, e.g. how frequently they joke in a similar manor, what they know about their trigger points or if there is a hidden struggle for power. I think for most couples this would be a harmless prank both can laugh about and kiss afterwards.
Honestly I would be angry too. But then after I would have completely woken up I would laugh about it. And think of a payback. Maybe even something involving a moist, cold sponge.
My brother-in-law once put a slice of bread on my sleeping sister's stomach, and when their dog (a very gluttonous beagle) started chowing down, woke her up by shaking her while shouting "the dog is eating your flesh!".