Okay, so everyone knows that wheelies are one of the purest forms of joy known to humanity, but could they be bad for your bike? That depends. As a rule, wheelies aren’t bad for your bike, but bad wheelies are.
What do I mean by bad wheelies? I'm talking about sloppy, jerky, uncontrolled wheelies where you're revving out the engine and dropping the clutch to get the front wheel up, then chopping the throttle, or worse yet riding it out to the rev limiter and slamming the front wheel down.
If that's how you're doing wheelies, please stop. Bad wheelies like that are torturing your clutch and causing excess wear on the friction plates and clutch basket, shock-loading your chain and sprockets, and hammering your fork. If you slam that front end down hard enough or often enough, you're liable to blow a fork seal. That means barfing oil all over your brakes and having to do a costly or time-consuming fork rebuild.
So are there non-harmful wheelies? Yes. Smooth, controlled wheelies where you lift the front with clutch finesse or pure horsepower and then set it down again gently aren’t going to do any harm to your bike. You see 600s, 1000s, and MotoGP bikes doing those kind of power wheelies all the time in racing. It’s just a function of accelerating hard enough that the bike begins to rotate up on the rear wheel.
Even if you’re as smooth as can be and have perfect technique and can ride wheelies for miles, it is possible that cruising with the front wheel four feet off the ground can starve your engine for oil. That’s not an issue for most bikes, but some models, like Suzuki’s SV650, are kind of famous for seizing due to oil starvation caused by extended wheelies. Yikes.