I agree that when the pranks are mean-spirited or annoying, it can be a drag, but, I feel like if its something inoffensive and everyone has fun with it, then its okay.
A few years ago, the prank was to have the whole site display upside-down, which annoyed me because it gave me a huge headache trying to use the site XD Compared to that, I'm pretty cool with these other April Fool's themes ^_^