Regarding the OP's claim that 'every skill has a counter', this is not entirely true. Most offensive abilities have some method of countering, but there are few ways of clearing defensive abilities. Subnuke is one of the few. Target has Tactical Team, EPtS2/3, and TSS2/3 up? Subnuke it. If they're a decent tank, they'll have a science team somewhere in there.
Subnuke is literally one of the very few ways to break a good tanker, someone who's got their defensive buffs chained together flawlessly and has great timing on their cycles. I don't like it when it's used on me in my Hegh'ta BoP, as that strikes me as overkill, but I sure do appreciate it when someone subnukes a target and I time a decloak alphastrike with it.
Yeah, you are right. I forgot about Plasmonic Leech. I have yet to find a counter for that.