The real problem about Lethality / Penetration.
The problem is not lethality itself. It's not armor penetration itself. The problem is that you can combine big amounts of both.
On one side, you have lethality, which is good against low armour targers, and you can conviniently get a maximum of 84 I believe. This is the armor scaling of a level 18 champion for most of them, essentially negating it. But, there are champions who build armour and those who don't. Those who don't will essentially take true damage, which is kind of a problem.
What about the ones who do build armour though? Let's say a tank with 400 armor. Great, you just now hit the tank with effectively reducing its armor to about 320. That's not a big deal either. In both cases, lethality itself isn't the problem. Squishies are still squishies, tanks still get to tank.
Now, let's see the whisper items themselves. Since the only work on bonus armour, they pretty much have 0 effect on squishies, which is perfect, no threat. On a 400 armor tank, which has 300 bonus armor, they are brought down to about 250, which is still slightly good.
The real problem is when you combine the two, and being able to do so without sacrificing a lot. Being able to deal both true damage to squishies through lethality and good damage on the tanks through armor pen is the problem. And the particular problem with it is that the values are too high. 84 lethality countering the armor of a squishy is a problem. 45% Bonus armor penetration is also a problem. But those are problematic situationally. When combining the two, you get to be problematic EVERYWHERE, against squishies and tanks, because the numbers are just so high, that they can't be countered.