I don't see anyway around it being a guessing game. The only thing that eases it up is that the majority of people netdeck card for card so you typically know the typical secrets based off other minions played,
It isn't about netdecking. It is about knowing what is good in the meta. Someone mentioned earlier that snake trap is not good in this meta. So if you have a situation where snake trap isn't a big deal, you probably don't play around it at all. But if snake trap is good in a particular meta, you probably should play around it. That is not guessing, that is playing smart and figuring out the odds and weighing it against the risks.
Knowing the lists people play is just secondary. You know what secrets work and what don't. That is basic card knowledge. If you're playing against a face hunter, you know its likely explosive trap. If you recognize it as a hybrid or midrange hunter, you know its probably freezing trap. Narrowing the possible traps is just smart play, not really just guessing. Because all the time you're evaluating risk and benefit. That is absolutely not guessing. At least it is no more guesswork than determining a certain line of play that wins based on the assumption your opponent has not drawn a particular card. It's like saying "hey, if you have molten giants I probably lose, but I definitely lose if I play around molten giants on this turn."
but ladder being a best-of-one gives a lot of advantage to tossing in something not super common like counterspell.
Sure, but on ladder you're playing for a high winrate over the course of many games. If you lose to some odd ball every once in a while, that is fine.
If you are against a mage that has a secret up and a minion(let's say water ele) and you're another mage with a piloted shredder or a fireball, most people play around mirror entity and would do a spell, but if the fireball gets blocked you just ate a card and your whole turn and that is a massive swing. And the whole thing was a 50/50 since either outcome is really bad for you.
It is hard to evaluate a board state just by knowing a few things. It depends on what is in your hand and how important it is to remove that water elemental this very turn. Yes, you probably lose if your fireball is CS'd but then if you had another reasonable play, you should take it. You're taking a 50/50 chance for it to be counterspell, but you lose if it is. If you have another reasonable play, like giving them a minion in mirror entity, perhaps even one you can remove with frostbolt, then you go with that. Once you see it isn't mirror entity, you can play with the knowledge that it is either effigy or counterspell and go from there.
In short, why take the 50/50 chance to lose, unless it is absolutely necessary and at that point it wasn't really counterspell that made you lose but how you got there (draw order, deck build, choices made, etc.). And certainly not a guessing game. It is evaluating risk.
Mad Scientist draws and puts the card into play which is even better than just drawing. It makes it super versatile in more than just aggro since a deck like Freeze mage can specifically cycle something like Ice Block out of the deck which actually strengthens their Arcane Intellect/Acolyte/other draw engines as the deck was specifically thinned even moreso. It being a 2/2 is crazy compared to the 2/1 loothoarder.
Sure, mad scientist is a great card. On the other hand, decks need something great about them in order to succeed. Compared to loot hoarder, you can say it is better. I don't disagree. But mad scientist is actually an extremely bad card at times, especially if you have played or drawn your secrets already. It is also a bigger loss when silenced.
Mage is one of my most played classes and even doing different lists I always tend to get free value out of the card. Druids playing around mirror entity with a super weak keeper of the grove that gets no value and then playing ancient of lore off curve next turn, stuff like that. And when you don't proc the secret and they play ANOTHER one their next turn you have to re-evaluate the options again, sometimes being a 50/50 like above where you only have a beefy minion or a beefy spell and have to chose one. Or against hunter the freeze trap lockdowns that mainly occur due to the tempo swing gained by the scientist.
Mages pretty much counter druid. And they should. And I am glad they do. But druids aren't helpless, seeing as they got one of the best counters to mirror entity - darnassus aspirant. And they've always had access to and often ran zombie chow in the past. Plus they do have a couple cheap cards that allow them to play around counterspell. Granted, they are playing a bad match up still. You kinda make it sound like druids don't have their own broken cards, like ancient of lore being incredibly great, as well as combo, innervating early big minions, etc..
I do think MC is way over statted for what he does as well, but scientist will always be the brunt of my rage towards it since it's a ridiculous card.
Good cards will always seem ridiculous in the right match up.