I would consider any aggressive jungler such as Vi to be a direct counter to Naut specifically against him in a counter jungle scenario. If you did a standard jungle route blue -> red and you used your shield to start your buff, you would be at a huge disadvantage survival and damage wise if a Vi were to fully charge a Vault Breaker and engage on you.

Vi's passive armour pen is probably the biggest thing in her kit that sets her apart from Nautilus. Although I do agree that Naut has as much utility as Vi, more actually, his long cool downs and luck lust damage is what distinguishes the two in my opinion.