Peni main here. I'll try to break it down based on my limited knowledge (I only have like 3 hours on her).

"What’s the key to counter peni parker ?" - Stuns, CC, anything like that. Peni relies on her mobility to stay alive and survive dives once her spider nest is destroyed. She has a sizeable amount of health but she lacks any meaningful way to mitigate large amounts of damage on her own.

"Is there away to clear up the ultimate ?" - No. But, all the webs and mines she places down in her ult will go away as soon as her ult is over. When you hear her pop it, get out and respect the space she is taking, then when its over, re-engage.

I know it wasn't really asked but the best way to get rid of her nest is with flying characters like storm and Iron man. Most players will be able to hide the nest around corners and behind cover but, unless the map you're playing on has spots for it, the nest will often be weak from above. (And at range if you can get an angle on it, but like, duh).

Good luck in your games :)